[1] "ofn"        "-oTLUAD-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/LUAD-TP/15084450/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/15246506/transformed.cor.cli.txt"

nPatients in clinical file=521, in cluster file=533, common to both=480
[1] "Reduce the number of clustering variables from 397 to 393."
[1] 393 480
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           255            225 
  TP53 MUTATED TP53 WILD-TYPE 
           255            225 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           150            330 
  KRAS MUTATED KRAS WILD-TYPE 
           150            330 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             84             396 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             84             396 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            67            413 
  EGFR MUTATED EGFR WILD-TYPE 
            67            413 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
             33             447 
  RBM10 MUTATED RBM10 WILD-TYPE 
             33             447 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               442 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               442 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             76             404 
  STK11 MUTATED STK11 WILD-TYPE 
             76             404 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           26           454 
  RB1 MUTATED RB1 WILD-TYPE 
           26           454 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              30              450 
  ARID1A MUTATED ARID1A WILD-TYPE 
              30              450 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           55           425 
  NF1 MUTATED NF1 WILD-TYPE 
           55           425 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            38            442 
  BRAF MUTATED BRAF WILD-TYPE 
            38            442 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           40           440 
  MGA MUTATED MGA WILD-TYPE 
           40           440 
[1] "CHRND MUTATION ANALYSIS"
[1] 3
  CHRND MUTATED CHRND WILD-TYPE 
             18             462 
  CHRND MUTATED CHRND WILD-TYPE 
             18             462 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           21           459 
  MET MUTATED MET WILD-TYPE 
           21           459 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              464 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              464 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             12             468 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             12             468 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             30             450 
  SETD2 MUTATED SETD2 WILD-TYPE 
             30             450 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              18              462 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              18              462 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             469 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             469 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           42           438 
  ATM MUTATED ATM WILD-TYPE 
           42           438 
[1] "COL5A2 MUTATION ANALYSIS"
[1] 3
  COL5A2 MUTATED COL5A2 WILD-TYPE 
              48              432 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
              48              432 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              467 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              467 
[1] "PPP3CA MUTATION ANALYSIS"
[1] 3
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              468 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              468 
[1] "FCRLA MUTATION ANALYSIS"
[1] 3
  FCRLA MUTATED FCRLA WILD-TYPE 
             15             465 
  FCRLA MUTATED FCRLA WILD-TYPE 
             15             465 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             456 
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             456 
[1] "SLAMF9 MUTATION ANALYSIS"
[1] 3
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              468 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              468 
[1] "SLC4A3 MUTATION ANALYSIS"
[1] 3
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              462 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              462 
[1] "SP100 MUTATION ANALYSIS"
[1] 3
  SP100 MUTATED SP100 WILD-TYPE 
             16             464 
  SP100 MUTATED SP100 WILD-TYPE 
             16             464 
[1] "RPL5 MUTATION ANALYSIS"
[1] 3
  RPL5 MUTATED RPL5 WILD-TYPE 
             8            472 
  RPL5 MUTATED RPL5 WILD-TYPE 
             8            472 
[1] "AACS MUTATION ANALYSIS"
[1] 3
  AACS MUTATED AACS WILD-TYPE 
            18            462 
  AACS MUTATED AACS WILD-TYPE 
            18            462 
[1] "ITGBL1 MUTATION ANALYSIS"
[1] 3
  ITGBL1 MUTATED ITGBL1 WILD-TYPE 
              19              461 
  ITGBL1 MUTATED ITGBL1 WILD-TYPE 
              19              461 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
             10             470 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
             10             470 
[1] "STIM1 MUTATION ANALYSIS"
[1] 3
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             471 
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             471 
[1] "NCKAP1L MUTATION ANALYSIS"
[1] 3
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               461 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               461 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              461 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              461 
[1] "PLEKHB2 MUTATION ANALYSIS"
[1] 3
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                9               471 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                9               471 
[1] "G3BP1 MUTATION ANALYSIS"
[1] 3
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              8             472 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              8             472 
[1] "TLR9 MUTATION ANALYSIS"
[1] 3
  TLR9 MUTATED TLR9 WILD-TYPE 
            10            470 
  TLR9 MUTATED TLR9 WILD-TYPE 
            10            470 
[1] "PDE6A MUTATION ANALYSIS"
[1] 3
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             464 
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             464 
[1] "DUSP22 MUTATION ANALYSIS"
[1] 3
  DUSP22 MUTATED DUSP22 WILD-TYPE 
              17              463 
  DUSP22 MUTATED DUSP22 WILD-TYPE 
              17              463 
[1] "MMP19 MUTATION ANALYSIS"
[1] 3
  MMP19 MUTATED MMP19 WILD-TYPE 
              9             471 
  MMP19 MUTATED MMP19 WILD-TYPE 
              9             471 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           20           460 
  APC MUTATED APC WILD-TYPE 
           20           460 
[1] "STRA8 MUTATION ANALYSIS"
[1] 3
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             472 
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             472 
[1] "A2M MUTATION ANALYSIS"
[1] 3
  A2M MUTATED A2M WILD-TYPE 
           20           460 
  A2M MUTATED A2M WILD-TYPE 
           20           460 
[1] "CD244 MUTATION ANALYSIS"
[1] 3
  CD244 MUTATED CD244 WILD-TYPE 
             12             468 
  CD244 MUTATED CD244 WILD-TYPE 
             12             468 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
            16            464 
  SRPX MUTATED SRPX WILD-TYPE 
            16            464 
[1] "GAGE2D MUTATION ANALYSIS"
[1] 3
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               5              475 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               5              475 
[1] "ADNP2 MUTATION ANALYSIS"
[1] 3
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             24             456 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             24             456 
[1] "GLDC MUTATION ANALYSIS"
[1] 3
  GLDC MUTATED GLDC WILD-TYPE 
            21            459 
  GLDC MUTATED GLDC WILD-TYPE 
            21            459 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              452 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              452 
[1] "MED12 MUTATION ANALYSIS"
[1] 3
  MED12 MUTATED MED12 WILD-TYPE 
             37             443 
  MED12 MUTATED MED12 WILD-TYPE 
             37             443 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              462 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              462 
[1] "DSC2 MUTATION ANALYSIS"
[1] 3
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            460 
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            460 
[1] "BTK MUTATION ANALYSIS"
[1] 3
  BTK MUTATED BTK WILD-TYPE 
           16           464 
  BTK MUTATED BTK WILD-TYPE 
           16           464 
[1] "KIF18B MUTATION ANALYSIS"
[1] 3
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              476 
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              476 
[1] "WDR66 MUTATION ANALYSIS"
[1] 3
  WDR66 MUTATED WDR66 WILD-TYPE 
             14             466 
  WDR66 MUTATED WDR66 WILD-TYPE 
             14             466 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            473 
  PTEN MUTATED PTEN WILD-TYPE 
             7            473 
[1] "LTBP1 MUTATION ANALYSIS"
[1] 3
  LTBP1 MUTATED LTBP1 WILD-TYPE 
             46             434 
  LTBP1 MUTATED LTBP1 WILD-TYPE 
             46             434 
[1] "C10ORF71 MUTATION ANALYSIS"
[1] 3
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                16                464 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                16                464 
[1] "KLHL5 MUTATION ANALYSIS"
[1] 3
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             466 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             466 
[1] "FAM65C MUTATION ANALYSIS"
[1] 3
  FAM65C MUTATED FAM65C WILD-TYPE 
              14              466 
  FAM65C MUTATED FAM65C WILD-TYPE 
              14              466 
[1] "KRTAP5-10 MUTATION ANALYSIS"
[1] 3
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                 12                 468 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                 12                 468 
[1] "PAK1 MUTATION ANALYSIS"
[1] 3
  PAK1 MUTATED PAK1 WILD-TYPE 
             9            471 
  PAK1 MUTATED PAK1 WILD-TYPE 
             9            471 
[1] "ABCC4 MUTATION ANALYSIS"
[1] 3
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             19             461 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             19             461 
[1] "HERC4 MUTATION ANALYSIS"
[1] 3
  HERC4 MUTATED HERC4 WILD-TYPE 
             13             467 
  HERC4 MUTATED HERC4 WILD-TYPE 
             13             467 
[1] "DMRTB1 MUTATION ANALYSIS"
[1] 3
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
              10              470 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
              10              470 
[1] "C5AR1 MUTATION ANALYSIS"
[1] 3
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              5             475 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              5             475 
[1] "SLC26A10 MUTATION ANALYSIS"
[1] 3
  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
                14                466 
  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
                14                466 
[1] "PTGIS MUTATION ANALYSIS"
[1] 3
  PTGIS MUTATED PTGIS WILD-TYPE 
             11             469 
  PTGIS MUTATED PTGIS WILD-TYPE 
             11             469 
[1] "DLX5 MUTATION ANALYSIS"
[1] 3
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            467 
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            467 
[1] "GPATCH4 MUTATION ANALYSIS"
[1] 3
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                8               472 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                8               472 
[1] "NR4A2 MUTATION ANALYSIS"
[1] 3
  NR4A2 MUTATED NR4A2 WILD-TYPE 
             17             463 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
             17             463 
[1] "ABHD12B MUTATION ANALYSIS"
[1] 3
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               473 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               473 
[1] "FNDC7 MUTATION ANALYSIS"
[1] 3
  FNDC7 MUTATED FNDC7 WILD-TYPE 
             10             470 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
             10             470 
[1] "RIT1 MUTATION ANALYSIS"
[1] 3
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            472 
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            472 
[1] "ASCL3 MUTATION ANALYSIS"
[1] 3
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             473 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             473 
[1] "CD84 MUTATION ANALYSIS"
[1] 3
  CD84 MUTATED CD84 WILD-TYPE 
             6            474 
  CD84 MUTATED CD84 WILD-TYPE 
             6            474 
[1] "GYPC MUTATION ANALYSIS"
[1] 3
  GYPC MUTATED GYPC WILD-TYPE 
             6            474 
  GYPC MUTATED GYPC WILD-TYPE 
             6            474 
[1] "MYH7 MUTATION ANALYSIS"
[1] 3
  MYH7 MUTATED MYH7 WILD-TYPE 
            51            429 
  MYH7 MUTATED MYH7 WILD-TYPE 
            51            429 
[1] "UROC1 MUTATION ANALYSIS"
[1] 3
  UROC1 MUTATED UROC1 WILD-TYPE 
             15             465 
  UROC1 MUTATED UROC1 WILD-TYPE 
             15             465 
[1] "HSF5 MUTATION ANALYSIS"
[1] 3
  HSF5 MUTATED HSF5 WILD-TYPE 
            13            467 
  HSF5 MUTATED HSF5 WILD-TYPE 
            13            467 
[1] "HSPA8 MUTATION ANALYSIS"
[1] 3
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             471 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             471 
[1] "HTRA1 MUTATION ANALYSIS"
[1] 3
  HTRA1 MUTATED HTRA1 WILD-TYPE 
             10             470 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
             10             470 
[1] "DST MUTATION ANALYSIS"
[1] 3
  DST MUTATED DST WILD-TYPE 
           89           391 
  DST MUTATED DST WILD-TYPE 
           89           391 
[1] "SRMS MUTATION ANALYSIS"
[1] 3
  SRMS MUTATED SRMS WILD-TYPE 
            10            470 
  SRMS MUTATED SRMS WILD-TYPE 
            10            470 
[1] "PTPRU MUTATION ANALYSIS"
[1] 3
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             462 
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             462 
[1] "ADAM10 MUTATION ANALYSIS"
[1] 3
  ADAM10 MUTATED ADAM10 WILD-TYPE 
               8              472 
  ADAM10 MUTATED ADAM10 WILD-TYPE 
               8              472 
[1] "MRPS35 MUTATION ANALYSIS"
[1] 3
  MRPS35 MUTATED MRPS35 WILD-TYPE 
               6              474 
  MRPS35 MUTATED MRPS35 WILD-TYPE 
               6              474 
[1] "ZNF608 MUTATION ANALYSIS"
[1] 3
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              471 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              471 
[1] "ARHGAP32 MUTATION ANALYSIS"
[1] 3
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                19                461 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                19                461 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             3            477 
  NRAS MUTATED NRAS WILD-TYPE 
             3            477 
[1] "HCLS1 MUTATION ANALYSIS"
[1] 3
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             16             464 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             16             464 
[1] "KIAA0895L MUTATION ANALYSIS"
[1] 3
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
                  4                 476 
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
                  4                 476 
[1] "BMP2K MUTATION ANALYSIS"
[1] 3
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             467 
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             467 
[1] "DOT1L MUTATION ANALYSIS"
[1] 3
  DOT1L MUTATED DOT1L WILD-TYPE 
             14             466 
  DOT1L MUTATED DOT1L WILD-TYPE 
             14             466 
[1] "SND1 MUTATION ANALYSIS"
[1] 3
  SND1 MUTATED SND1 WILD-TYPE 
            16            464 
  SND1 MUTATED SND1 WILD-TYPE 
            16            464 
[1] "VGLL3 MUTATION ANALYSIS"
[1] 3
  VGLL3 MUTATED VGLL3 WILD-TYPE 
             17             463 
  VGLL3 MUTATED VGLL3 WILD-TYPE 
             17             463 
[1] "LUM MUTATION ANALYSIS"
[1] 3
  LUM MUTATED LUM WILD-TYPE 
           15           465 
  LUM MUTATED LUM WILD-TYPE 
           15           465 
[1] "ATP1B4 MUTATION ANALYSIS"
[1] 3
  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
               9              471 
  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
               9              471 
[1] "ATAD2 MUTATION ANALYSIS"
[1] 3
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             14             466 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             14             466 
[1] "SLC17A9 MUTATION ANALYSIS"
[1] 3
  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
                8               472 
  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
                8               472 
[1] "ZNF592 MUTATION ANALYSIS"
[1] 3
  ZNF592 MUTATED ZNF592 WILD-TYPE 
              16              464 
  ZNF592 MUTATED ZNF592 WILD-TYPE 
              16              464 
[1] "ZNF556 MUTATION ANALYSIS"
[1] 3
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              468 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              468 
[1] "ZEB1 MUTATION ANALYSIS"
[1] 3
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            32            448 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            32            448 
[1] "SLC22A6 MUTATION ANALYSIS"
[1] 3
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               14               466 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               14               466 
[1] "RABEPK MUTATION ANALYSIS"
[1] 3
  RABEPK MUTATED RABEPK WILD-TYPE 
               6              474 
  RABEPK MUTATED RABEPK WILD-TYPE 
               6              474 
[1] "CHGB MUTATION ANALYSIS"
[1] 3
  CHGB MUTATED CHGB WILD-TYPE 
            14            466 
  CHGB MUTATED CHGB WILD-TYPE 
            14            466 
[1] "ESYT3 MUTATION ANALYSIS"
[1] 3
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             472 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             472 
[1] "L1CAM MUTATION ANALYSIS"
[1] 3
  L1CAM MUTATED L1CAM WILD-TYPE 
             34             446 
  L1CAM MUTATED L1CAM WILD-TYPE 
             34             446 
[1] "SLC17A3 MUTATION ANALYSIS"
[1] 3
  SLC17A3 MUTATED SLC17A3 WILD-TYPE 
               15               465 
  SLC17A3 MUTATED SLC17A3 WILD-TYPE 
               15               465 
[1] "ITIH2 MUTATION ANALYSIS"
[1] 3
  ITIH2 MUTATED ITIH2 WILD-TYPE 
             19             461 
  ITIH2 MUTATED ITIH2 WILD-TYPE 
             19             461 
[1] "HP1BP3 MUTATION ANALYSIS"
[1] 3
  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
               8              472 
  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
               8              472 
[1] "LAMA4 MUTATION ANALYSIS"
[1] 3
  LAMA4 MUTATED LAMA4 WILD-TYPE 
             34             446 
  LAMA4 MUTATED LAMA4 WILD-TYPE 
             34             446 
[1] "TMCO2 MUTATION ANALYSIS"
[1] 3
  TMCO2 MUTATED TMCO2 WILD-TYPE 
              6             474 
  TMCO2 MUTATED TMCO2 WILD-TYPE 
              6             474 
[1] "N4BP1 MUTATION ANALYSIS"
[1] 3
  N4BP1 MUTATED N4BP1 WILD-TYPE 
              9             471 
  N4BP1 MUTATED N4BP1 WILD-TYPE 
              9             471 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             467 
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             467 
[1] "ZACN MUTATION ANALYSIS"
[1] 3
  ZACN MUTATED ZACN WILD-TYPE 
             8            472 
  ZACN MUTATED ZACN WILD-TYPE 
             8            472 
[1] "SFTPB MUTATION ANALYSIS"
[1] 3
  SFTPB MUTATED SFTPB WILD-TYPE 
              6             474 
  SFTPB MUTATED SFTPB WILD-TYPE 
              6             474 
[1] "SRRM3 MUTATION ANALYSIS"
[1] 3
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              5             475 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              5             475 
[1] "FAM71A MUTATION ANALYSIS"
[1] 3
  FAM71A MUTATED FAM71A WILD-TYPE 
              15              465 
  FAM71A MUTATED FAM71A WILD-TYPE 
              15              465 
[1] "MCM9 MUTATION ANALYSIS"
[1] 3
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            477 
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            477 
[1] "GRAP2 MUTATION ANALYSIS"
[1] 3
  GRAP2 MUTATED GRAP2 WILD-TYPE 
             11             469 
  GRAP2 MUTATED GRAP2 WILD-TYPE 
             11             469 
[1] "ARHGAP4 MUTATION ANALYSIS"
[1] 3
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
               14               466 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
               14               466 
[1] "IFI35 MUTATION ANALYSIS"
[1] 3
  IFI35 MUTATED IFI35 WILD-TYPE 
              3             477 
  IFI35 MUTATED IFI35 WILD-TYPE 
              3             477 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
             15             465 
  CDK12 MUTATED CDK12 WILD-TYPE 
             15             465 
[1] "TMEM202 MUTATION ANALYSIS"
[1] 3
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                6               474 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                6               474 
[1] "GTF2A1 MUTATION ANALYSIS"
[1] 3
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
               3              477 
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
               3              477 
[1] "SERPINB13 MUTATION ANALYSIS"
[1] 3
  SERPINB13 MUTATED SERPINB13 WILD-TYPE 
                 10                 470 
  SERPINB13 MUTATED SERPINB13 WILD-TYPE 
                 10                 470 
[1] "RAMP2 MUTATION ANALYSIS"
[1] 3
  RAMP2 MUTATED RAMP2 WILD-TYPE 
              3             477 
  RAMP2 MUTATED RAMP2 WILD-TYPE 
              3             477 
[1] "RNASEH1 MUTATION ANALYSIS"
[1] 3
  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
                6               474 
  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
                6               474 
[1] "GLTSCR1 MUTATION ANALYSIS"
[1] 3
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                8               472 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                8               472 
[1] "PDE1A MUTATION ANALYSIS"
[1] 3
  PDE1A MUTATED PDE1A WILD-TYPE 
             15             465 
  PDE1A MUTATED PDE1A WILD-TYPE 
             15             465 
[1] "SATB2 MUTATION ANALYSIS"
[1] 3
  SATB2 MUTATED SATB2 WILD-TYPE 
             31             449 
  SATB2 MUTATED SATB2 WILD-TYPE 
             31             449 
[1] "RAF1 MUTATION ANALYSIS"
[1] 3
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            474 
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            474 
[1] "PLXND1 MUTATION ANALYSIS"
[1] 3
  PLXND1 MUTATED PLXND1 WILD-TYPE 
              15              465 
  PLXND1 MUTATED PLXND1 WILD-TYPE 
              15              465 
[1] "OFD1 MUTATION ANALYSIS"
[1] 3
  OFD1 MUTATED OFD1 WILD-TYPE 
            15            465 
  OFD1 MUTATED OFD1 WILD-TYPE 
            15            465 
[1] "APLF MUTATION ANALYSIS"
[1] 3
  APLF MUTATED APLF WILD-TYPE 
             4            476 
  APLF MUTATED APLF WILD-TYPE 
             4            476 
[1] "ADAMTS2 MUTATION ANALYSIS"
[1] 3
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               39               441 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               39               441 
[1] "CAPN11 MUTATION ANALYSIS"
[1] 3
  CAPN11 MUTATED CAPN11 WILD-TYPE 
              12              468 
  CAPN11 MUTATED CAPN11 WILD-TYPE 
              12              468 
[1] "FLCN MUTATION ANALYSIS"
[1] 3
  FLCN MUTATED FLCN WILD-TYPE 
            10            470 
  FLCN MUTATED FLCN WILD-TYPE 
            10            470 
[1] "C2ORF53 MUTATION ANALYSIS"
[1] 3
  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
               13               467 
  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
               13               467 
[1] "C1ORF177 MUTATION ANALYSIS"
[1] 3
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                 9                471 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                 9                471 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
              5             475 
  STK19 MUTATED STK19 WILD-TYPE 
              5             475 
[1] "PKD2 MUTATION ANALYSIS"
[1] 3
  PKD2 MUTATED PKD2 WILD-TYPE 
            15            465 
  PKD2 MUTATED PKD2 WILD-TYPE 
            15            465 
[1] "NOTCH4 MUTATION ANALYSIS"
[1] 3
  NOTCH4 MUTATED NOTCH4 WILD-TYPE 
              43              437 
  NOTCH4 MUTATED NOTCH4 WILD-TYPE 
              43              437 
[1] "COL15A1 MUTATION ANALYSIS"
[1] 3
  COL15A1 MUTATED COL15A1 WILD-TYPE 
               31               449 
  COL15A1 MUTATED COL15A1 WILD-TYPE 
               31               449 
[1] "SOS2 MUTATION ANALYSIS"
[1] 3
  SOS2 MUTATED SOS2 WILD-TYPE 
            13            467 
  SOS2 MUTATED SOS2 WILD-TYPE 
            13            467 
[1] "SETDB1 MUTATION ANALYSIS"
[1] 3
  SETDB1 MUTATED SETDB1 WILD-TYPE 
              10              470 
  SETDB1 MUTATED SETDB1 WILD-TYPE 
              10              470 
[1] "ANTXR1 MUTATION ANALYSIS"
[1] 3
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              461 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              461 
[1] "SLC38A8 MUTATION ANALYSIS"
[1] 3
  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
                9               471 
  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
                9               471 
[1] "COL3A1 MUTATION ANALYSIS"
[1] 3
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              53              427 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              53              427 
[1] "RBBP6 MUTATION ANALYSIS"
[1] 3
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             17             463 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             17             463 
[1] "RFX1 MUTATION ANALYSIS"
[1] 3
  RFX1 MUTATED RFX1 WILD-TYPE 
             9            471 
  RFX1 MUTATED RFX1 WILD-TYPE 
             9            471 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
            13            467 
  PRB2 MUTATED PRB2 WILD-TYPE 
            13            467 
[1] "COL25A1 MUTATION ANALYSIS"
[1] 3
  COL25A1 MUTATED COL25A1 WILD-TYPE 
               32               448 
  COL25A1 MUTATED COL25A1 WILD-TYPE 
               32               448 
[1] "PPP2R5B MUTATION ANALYSIS"
[1] 3
  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
                7               473 
  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
                7               473 
[1] "DZIP1L MUTATION ANALYSIS"
[1] 3
  DZIP1L MUTATED DZIP1L WILD-TYPE 
              11              469 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
              11              469 
[1] "RLTPR MUTATION ANALYSIS"
[1] 3
  RLTPR MUTATED RLTPR WILD-TYPE 
             15             465 
  RLTPR MUTATED RLTPR WILD-TYPE 
             15             465 
[1] "CD40LG MUTATION ANALYSIS"
[1] 3
  CD40LG MUTATED CD40LG WILD-TYPE 
               6              474 
  CD40LG MUTATED CD40LG WILD-TYPE 
               6              474 
[1] "LGALS2 MUTATION ANALYSIS"
[1] 3
  LGALS2 MUTATED LGALS2 WILD-TYPE 
               5              475 
  LGALS2 MUTATED LGALS2 WILD-TYPE 
               5              475 
[1] "PADI2 MUTATION ANALYSIS"
[1] 3
  PADI2 MUTATED PADI2 WILD-TYPE 
             10             470 
  PADI2 MUTATED PADI2 WILD-TYPE 
             10             470 
[1] "C1ORF116 MUTATION ANALYSIS"
[1] 3
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                11                469 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                11                469 
[1] "NBPF3 MUTATION ANALYSIS"
[1] 3
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              6             474 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              6             474 
[1] "RNMT MUTATION ANALYSIS"
[1] 3
  RNMT MUTATED RNMT WILD-TYPE 
             7            473 
  RNMT MUTATED RNMT WILD-TYPE 
             7            473 
[1] "PXK MUTATION ANALYSIS"
[1] 3
  PXK MUTATED PXK WILD-TYPE 
            7           473 
  PXK MUTATED PXK WILD-TYPE 
            7           473 
[1] "ZNF223 MUTATION ANALYSIS"
[1] 3
  ZNF223 MUTATED ZNF223 WILD-TYPE 
              10              470 
  ZNF223 MUTATED ZNF223 WILD-TYPE 
              10              470 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             462 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             462 
[1] "CPA4 MUTATION ANALYSIS"
[1] 3
  CPA4 MUTATED CPA4 WILD-TYPE 
            14            466 
  CPA4 MUTATED CPA4 WILD-TYPE 
            14            466 
[1] "SNX9 MUTATION ANALYSIS"
[1] 3
  SNX9 MUTATED SNX9 WILD-TYPE 
             7            473 
  SNX9 MUTATED SNX9 WILD-TYPE 
             7            473 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             8            472 
  BAP1 MUTATED BAP1 WILD-TYPE 
             8            472 
[1] "PCSK4 MUTATION ANALYSIS"
[1] 3
  PCSK4 MUTATED PCSK4 WILD-TYPE 
              8             472 
  PCSK4 MUTATED PCSK4 WILD-TYPE 
              8             472 
[1] "FOLH1 MUTATION ANALYSIS"
[1] 3
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             28             452 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             28             452 
[1] "ERLIN2 MUTATION ANALYSIS"
[1] 3
  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
               6              474 
  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
               6              474 
[1] "SBSN MUTATION ANALYSIS"
[1] 3
  SBSN MUTATED SBSN WILD-TYPE 
            12            468 
  SBSN MUTATED SBSN WILD-TYPE 
            12            468 
[1] "NID2 MUTATION ANALYSIS"
[1] 3
  NID2 MUTATED NID2 WILD-TYPE 
            33            447 
  NID2 MUTATED NID2 WILD-TYPE 
            33            447 
[1] "SAMD7 MUTATION ANALYSIS"
[1] 3
  SAMD7 MUTATED SAMD7 WILD-TYPE 
             11             469 
  SAMD7 MUTATED SAMD7 WILD-TYPE 
             11             469 
[1] "SERPINB5 MUTATION ANALYSIS"
[1] 3
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 9                471 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 9                471 
[1] "SLC39A6 MUTATION ANALYSIS"
[1] 3
  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
               14               466 
  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
               14               466 
[1] "PHKA1 MUTATION ANALYSIS"
[1] 3
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             468 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             468 
[1] "KRT26 MUTATION ANALYSIS"
[1] 3
  KRT26 MUTATED KRT26 WILD-TYPE 
              9             471 
  KRT26 MUTATED KRT26 WILD-TYPE 
              9             471 
[1] "CALCRL MUTATION ANALYSIS"
[1] 3
  CALCRL MUTATED CALCRL WILD-TYPE 
              13              467 
  CALCRL MUTATED CALCRL WILD-TYPE 
              13              467 
[1] "STRN3 MUTATION ANALYSIS"
[1] 3
  STRN3 MUTATED STRN3 WILD-TYPE 
             10             470 
  STRN3 MUTATED STRN3 WILD-TYPE 
             10             470 
[1] "RPS16 MUTATION ANALYSIS"
[1] 3
  RPS16 MUTATED RPS16 WILD-TYPE 
              3             477 
  RPS16 MUTATED RPS16 WILD-TYPE 
              3             477 
[1] "NPR1 MUTATION ANALYSIS"
[1] 3
  NPR1 MUTATED NPR1 WILD-TYPE 
            14            466 
  NPR1 MUTATED NPR1 WILD-TYPE 
            14            466 
[1] "KARS MUTATION ANALYSIS"
[1] 3
  KARS MUTATED KARS WILD-TYPE 
             7            473 
  KARS MUTATED KARS WILD-TYPE 
             7            473 
[1] "FRMD6 MUTATION ANALYSIS"
[1] 3
  FRMD6 MUTATED FRMD6 WILD-TYPE 
             14             466 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
             14             466 
[1] "TMC4 MUTATION ANALYSIS"
[1] 3
  TMC4 MUTATED TMC4 WILD-TYPE 
             9            471 
  TMC4 MUTATED TMC4 WILD-TYPE 
             9            471 
[1] "ARMC3 MUTATION ANALYSIS"
[1] 3
  ARMC3 MUTATED ARMC3 WILD-TYPE 
             22             458 
  ARMC3 MUTATED ARMC3 WILD-TYPE 
             22             458 
[1] "PIK3R4 MUTATION ANALYSIS"
[1] 3
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              20              460 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              20              460 
[1] "ESRP1 MUTATION ANALYSIS"
[1] 3
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              8             472 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              8             472 
[1] "GRN MUTATION ANALYSIS"
[1] 3
  GRN MUTATED GRN WILD-TYPE 
            6           474 
  GRN MUTATED GRN WILD-TYPE 
            6           474 
[1] "CYTH4 MUTATION ANALYSIS"
[1] 3
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              5             475 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              5             475 
[1] "SEC23IP MUTATION ANALYSIS"
[1] 3
  SEC23IP MUTATED SEC23IP WILD-TYPE 
                9               471 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
                9               471 
[1] "LARP4 MUTATION ANALYSIS"
[1] 3
  LARP4 MUTATED LARP4 WILD-TYPE 
              9             471 
  LARP4 MUTATED LARP4 WILD-TYPE 
              9             471 
[1] "SLAMF8 MUTATION ANALYSIS"
[1] 3
  SLAMF8 MUTATED SLAMF8 WILD-TYPE 
               9              471 
  SLAMF8 MUTATED SLAMF8 WILD-TYPE 
               9              471 
[1] "IGDCC4 MUTATION ANALYSIS"
[1] 3
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
              24              456 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
              24              456 
[1] "NPBWR2 MUTATION ANALYSIS"
[1] 3
  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
               8              472 
  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
               8              472 
[1] "FLRT3 MUTATION ANALYSIS"
[1] 3
  FLRT3 MUTATED FLRT3 WILD-TYPE 
              8             472 
  FLRT3 MUTATED FLRT3 WILD-TYPE 
              8             472 
[1] "MYO1G MUTATION ANALYSIS"
[1] 3
  MYO1G MUTATED MYO1G WILD-TYPE 
             12             468 
  MYO1G MUTATED MYO1G WILD-TYPE 
             12             468 
[1] "PUM2 MUTATION ANALYSIS"
[1] 3
  PUM2 MUTATED PUM2 WILD-TYPE 
            12            468 
  PUM2 MUTATED PUM2 WILD-TYPE 
            12            468 
[1] "C11ORF63 MUTATION ANALYSIS"
[1] 3
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                18                462 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                18                462 
[1] "IPP MUTATION ANALYSIS"
[1] 3
  IPP MUTATED IPP WILD-TYPE 
            5           475 
  IPP MUTATED IPP WILD-TYPE 
            5           475 
[1] "XRCC6 MUTATION ANALYSIS"
[1] 3
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              8             472 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              8             472 
[1] "RHEB MUTATION ANALYSIS"
[1] 3
  RHEB MUTATED RHEB WILD-TYPE 
             4            476 
  RHEB MUTATED RHEB WILD-TYPE 
             4            476 
[1] "TSLP MUTATION ANALYSIS"
[1] 3
  TSLP MUTATED TSLP WILD-TYPE 
             7            473 
  TSLP MUTATED TSLP WILD-TYPE 
             7            473 
[1] "LIPG MUTATION ANALYSIS"
[1] 3
  LIPG MUTATED LIPG WILD-TYPE 
             9            471 
  LIPG MUTATED LIPG WILD-TYPE 
             9            471 
[1] "SOS1 MUTATION ANALYSIS"
[1] 3
  SOS1 MUTATED SOS1 WILD-TYPE 
            14            466 
  SOS1 MUTATED SOS1 WILD-TYPE 
            14            466 
[1] "KCTD1 MUTATION ANALYSIS"
[1] 3
  KCTD1 MUTATED KCTD1 WILD-TYPE 
              6             474 
  KCTD1 MUTATED KCTD1 WILD-TYPE 
              6             474 
[1] "IRF2BP2 MUTATION ANALYSIS"
[1] 3
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                7               473 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                7               473 
[1] "SUN1 MUTATION ANALYSIS"
[1] 3
  SUN1 MUTATED SUN1 WILD-TYPE 
            15            465 
  SUN1 MUTATED SUN1 WILD-TYPE 
            15            465 
[1] "SEMA6C MUTATION ANALYSIS"
[1] 3
  SEMA6C MUTATED SEMA6C WILD-TYPE 
               7              473 
  SEMA6C MUTATED SEMA6C WILD-TYPE 
               7              473 
[1] "KLF5 MUTATION ANALYSIS"
[1] 3
  KLF5 MUTATED KLF5 WILD-TYPE 
             4            476 
  KLF5 MUTATED KLF5 WILD-TYPE 
             4            476 
[1] "RFTN2 MUTATION ANALYSIS"
[1] 3
  RFTN2 MUTATED RFTN2 WILD-TYPE 
             11             469 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
             11             469 
[1] "ZNF81 MUTATION ANALYSIS"
[1] 3
  ZNF81 MUTATED ZNF81 WILD-TYPE 
              7             473 
  ZNF81 MUTATED ZNF81 WILD-TYPE 
              7             473 
[1] "FER MUTATION ANALYSIS"
[1] 3
  FER MUTATED FER WILD-TYPE 
           13           467 
  FER MUTATED FER WILD-TYPE 
           13           467 
[1] "NPHS1 MUTATION ANALYSIS"
[1] 3
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             24             456 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             24             456 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
           42           438 
  KDR MUTATED KDR WILD-TYPE 
           42           438 
[1] "LDB2 MUTATION ANALYSIS"
[1] 3
  LDB2 MUTATED LDB2 WILD-TYPE 
            19            461 
  LDB2 MUTATED LDB2 WILD-TYPE 
            19            461 
[1] "FIBP MUTATION ANALYSIS"
[1] 3
  FIBP MUTATED FIBP WILD-TYPE 
             5            475 
  FIBP MUTATED FIBP WILD-TYPE 
             5            475 
[1] "MSH2 MUTATION ANALYSIS"
[1] 3
  MSH2 MUTATED MSH2 WILD-TYPE 
            11            469 
  MSH2 MUTATED MSH2 WILD-TYPE 
            11            469 
[1] "PARD3B MUTATION ANALYSIS"
[1] 3
  PARD3B MUTATED PARD3B WILD-TYPE 
              27              453 
  PARD3B MUTATED PARD3B WILD-TYPE 
              27              453 
[1] "LARS MUTATION ANALYSIS"
[1] 3
  LARS MUTATED LARS WILD-TYPE 
             7            473 
  LARS MUTATED LARS WILD-TYPE 
             7            473 
[1] "LCE2B MUTATION ANALYSIS"
[1] 3
  LCE2B MUTATED LCE2B WILD-TYPE 
              8             472 
  LCE2B MUTATED LCE2B WILD-TYPE 
              8             472 
[1] "NTHL1 MUTATION ANALYSIS"
[1] 3
  NTHL1 MUTATED NTHL1 WILD-TYPE 
              6             474 
  NTHL1 MUTATED NTHL1 WILD-TYPE 
              6             474 
[1] "UBAP2 MUTATION ANALYSIS"
[1] 3
  UBAP2 MUTATED UBAP2 WILD-TYPE 
             11             469 
  UBAP2 MUTATED UBAP2 WILD-TYPE 
             11             469 
[1] "MATR3 MUTATION ANALYSIS"
[1] 3
  MATR3 MUTATED MATR3 WILD-TYPE 
              7             473 
  MATR3 MUTATED MATR3 WILD-TYPE 
              7             473 
[1] "CD34 MUTATION ANALYSIS"
[1] 3
  CD34 MUTATED CD34 WILD-TYPE 
            10            470 
  CD34 MUTATED CD34 WILD-TYPE 
            10            470 
[1] "BRD9 MUTATION ANALYSIS"
[1] 3
  BRD9 MUTATED BRD9 WILD-TYPE 
             5            475 
  BRD9 MUTATED BRD9 WILD-TYPE 
             5            475 
[1] "BTAF1 MUTATION ANALYSIS"
[1] 3
  BTAF1 MUTATED BTAF1 WILD-TYPE 
             23             457 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
             23             457 
[1] "RGS20 MUTATION ANALYSIS"
[1] 3
  RGS20 MUTATED RGS20 WILD-TYPE 
              7             473 
  RGS20 MUTATED RGS20 WILD-TYPE 
              7             473 
[1] "ITLN1 MUTATION ANALYSIS"
[1] 3
  ITLN1 MUTATED ITLN1 WILD-TYPE 
              9             471 
  ITLN1 MUTATED ITLN1 WILD-TYPE 
              9             471 
[1] "FIGNL1 MUTATION ANALYSIS"
[1] 3
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              11              469 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              11              469 
[1] "ABCF3 MUTATION ANALYSIS"
[1] 3
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              8             472 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              8             472 
[1] "KSR1 MUTATION ANALYSIS"
[1] 3
  KSR1 MUTATED KSR1 WILD-TYPE 
            12            468 
  KSR1 MUTATED KSR1 WILD-TYPE 
            12            468 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             17             463 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             17             463 
[1] "IPO9 MUTATION ANALYSIS"
[1] 3
  IPO9 MUTATED IPO9 WILD-TYPE 
             9            471 
  IPO9 MUTATED IPO9 WILD-TYPE 
             9            471 
[1] "SLC26A4 MUTATION ANALYSIS"
[1] 3
  SLC26A4 MUTATED SLC26A4 WILD-TYPE 
               11               469 
  SLC26A4 MUTATED SLC26A4 WILD-TYPE 
               11               469 
[1] "MOCOS MUTATION ANALYSIS"
[1] 3
  MOCOS MUTATED MOCOS WILD-TYPE 
              9             471 
  MOCOS MUTATED MOCOS WILD-TYPE 
              9             471 
[1] "MOGAT2 MUTATION ANALYSIS"
[1] 3
  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
               8              472 
  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
               8              472 
[1] "ZKSCAN5 MUTATION ANALYSIS"
[1] 3
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                7               473 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                7               473 
[1] "GPR150 MUTATION ANALYSIS"
[1] 3
  GPR150 MUTATED GPR150 WILD-TYPE 
               3              477 
  GPR150 MUTATED GPR150 WILD-TYPE 
               3              477 
[1] "MGAT5B MUTATION ANALYSIS"
[1] 3
  MGAT5B MUTATED MGAT5B WILD-TYPE 
              19              461 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
              19              461 
[1] "AGXT MUTATION ANALYSIS"
[1] 3
  AGXT MUTATED AGXT WILD-TYPE 
             8            472 
  AGXT MUTATED AGXT WILD-TYPE 
             8            472 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8             472 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8             472 
[1] "CREB5 MUTATION ANALYSIS"
[1] 3
  CREB5 MUTATED CREB5 WILD-TYPE 
             13             467 
  CREB5 MUTATED CREB5 WILD-TYPE 
             13             467 
[1] "CD300E MUTATION ANALYSIS"
[1] 3
  CD300E MUTATED CD300E WILD-TYPE 
               7              473 
  CD300E MUTATED CD300E WILD-TYPE 
               7              473 
[1] "ZNF623 MUTATION ANALYSIS"
[1] 3
  ZNF623 MUTATED ZNF623 WILD-TYPE 
               9              471 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
               9              471 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                9               471 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                9               471 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
             17             463 
  BCL9L MUTATED BCL9L WILD-TYPE 
             17             463 
[1] "ZFP36L1 MUTATION ANALYSIS"
[1] 3
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               11               469 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               11               469 
[1] "PALM MUTATION ANALYSIS"
[1] 3
  PALM MUTATED PALM WILD-TYPE 
             6            474 
  PALM MUTATED PALM WILD-TYPE 
             6            474 
[1] "CSNK1A1L MUTATION ANALYSIS"
[1] 3
  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE 
                13                467 
  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE 
                13                467 
[1] "SCML4 MUTATION ANALYSIS"
[1] 3
  SCML4 MUTATED SCML4 WILD-TYPE 
             11             469 
  SCML4 MUTATED SCML4 WILD-TYPE 
             11             469 
[1] "SLC11A1 MUTATION ANALYSIS"
[1] 3
  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
                7               473 
  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
                7               473 
[1] "MOGAT3 MUTATION ANALYSIS"
[1] 3
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
              10              470 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
              10              470 
[1] "TULP4 MUTATION ANALYSIS"
[1] 3
  TULP4 MUTATED TULP4 WILD-TYPE 
             13             467 
  TULP4 MUTATED TULP4 WILD-TYPE 
             13             467 
[1] "ASB5 MUTATION ANALYSIS"
[1] 3
  ASB5 MUTATED ASB5 WILD-TYPE 
            14            466 
  ASB5 MUTATED ASB5 WILD-TYPE 
            14            466 
[1] "TDRD6 MUTATION ANALYSIS"
[1] 3
  TDRD6 MUTATED TDRD6 WILD-TYPE 
             17             463 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
             17             463 
[1] "COL12A1 MUTATION ANALYSIS"
[1] 3
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               54               426 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               54               426 
[1] "SMOC1 MUTATION ANALYSIS"
[1] 3
  SMOC1 MUTATED SMOC1 WILD-TYPE 
             12             468 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
             12             468 
[1] "HSD11B1 MUTATION ANALYSIS"
[1] 3
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                7               473 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                7               473 
[1] "COL7A1 MUTATION ANALYSIS"
[1] 3
  COL7A1 MUTATED COL7A1 WILD-TYPE 
              32              448 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
              32              448 
[1] "C1ORF105 MUTATION ANALYSIS"
[1] 3
  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
                 4                476 
  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
                 4                476 
[1] "NDUFB11 MUTATION ANALYSIS"
[1] 3
  NDUFB11 MUTATED NDUFB11 WILD-TYPE 
                6               474 
  NDUFB11 MUTATED NDUFB11 WILD-TYPE 
                6               474 
[1] "CHM MUTATION ANALYSIS"
[1] 3
  CHM MUTATED CHM WILD-TYPE 
           16           464 
  CHM MUTATED CHM WILD-TYPE 
           16           464 
[1] "TFDP1 MUTATION ANALYSIS"
[1] 3
  TFDP1 MUTATED TFDP1 WILD-TYPE 
              7             473 
  TFDP1 MUTATED TFDP1 WILD-TYPE 
              7             473 
[1] "NLGN2 MUTATION ANALYSIS"
[1] 3
  NLGN2 MUTATED NLGN2 WILD-TYPE 
              9             471 
  NLGN2 MUTATED NLGN2 WILD-TYPE 
              9             471 
[1] "PLEKHG5 MUTATION ANALYSIS"
[1] 3
  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
                7               473 
  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
                7               473 
[1] "OR5P3 MUTATION ANALYSIS"
[1] 3
  OR5P3 MUTATED OR5P3 WILD-TYPE 
              3             477 
  OR5P3 MUTATED OR5P3 WILD-TYPE 
              3             477 
[1] "CHD5 MUTATION ANALYSIS"
[1] 3
  CHD5 MUTATED CHD5 WILD-TYPE 
            30            450 
  CHD5 MUTATED CHD5 WILD-TYPE 
            30            450 
[1] "FBXO34 MUTATION ANALYSIS"
[1] 3
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               6              474 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               6              474 
[1] "TXLNB MUTATION ANALYSIS"
[1] 3
  TXLNB MUTATED TXLNB WILD-TYPE 
             17             463 
  TXLNB MUTATED TXLNB WILD-TYPE 
             17             463 
[1] "HSPA1L MUTATION ANALYSIS"
[1] 3
  HSPA1L MUTATED HSPA1L WILD-TYPE 
              10              470 
  HSPA1L MUTATED HSPA1L WILD-TYPE 
              10              470 
[1] "NUMA1 MUTATION ANALYSIS"
[1] 3
  NUMA1 MUTATED NUMA1 WILD-TYPE 
             17             463 
  NUMA1 MUTATED NUMA1 WILD-TYPE 
             17             463 
[1] "MEFV MUTATION ANALYSIS"
[1] 3
  MEFV MUTATED MEFV WILD-TYPE 
            17            463 
  MEFV MUTATED MEFV WILD-TYPE 
            17            463 
[1] "GAN MUTATION ANALYSIS"
[1] 3
  GAN MUTATED GAN WILD-TYPE 
           10           470 
  GAN MUTATED GAN WILD-TYPE 
           10           470 
[1] "SQSTM1 MUTATION ANALYSIS"
[1] 3
  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
               6              474 
  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
               6              474 
[1] "DSN1 MUTATION ANALYSIS"
[1] 3
  DSN1 MUTATED DSN1 WILD-TYPE 
             6            474 
  DSN1 MUTATED DSN1 WILD-TYPE 
             6            474 
[1] "NAAA MUTATION ANALYSIS"
[1] 3
  NAAA MUTATED NAAA WILD-TYPE 
             3            477 
  NAAA MUTATED NAAA WILD-TYPE 
             3            477 
[1] "GART MUTATION ANALYSIS"
[1] 3
  GART MUTATED GART WILD-TYPE 
             6            474 
  GART MUTATED GART WILD-TYPE 
             6            474 
[1] "TARBP1 MUTATION ANALYSIS"
[1] 3
  TARBP1 MUTATED TARBP1 WILD-TYPE 
              14              466 
  TARBP1 MUTATED TARBP1 WILD-TYPE 
              14              466 
[1] "HLA-DQA2 MUTATION ANALYSIS"
[1] 3
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
                 3                477 
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
                 3                477 
[1] "AHDC1 MUTATION ANALYSIS"
[1] 3
  AHDC1 MUTATED AHDC1 WILD-TYPE 
             10             470 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
             10             470 
[1] "ARHGEF12 MUTATION ANALYSIS"
[1] 3
  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE 
                21                459 
  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE 
                21                459 
[1] "UHRF1BP1L MUTATION ANALYSIS"
[1] 3
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 16                 464 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 16                 464 
[1] "HERC3 MUTATION ANALYSIS"
[1] 3
  HERC3 MUTATED HERC3 WILD-TYPE 
              8             472 
  HERC3 MUTATED HERC3 WILD-TYPE 
              8             472 
[1] "GALNT14 MUTATION ANALYSIS"
[1] 3
  GALNT14 MUTATED GALNT14 WILD-TYPE 
               20               460 
  GALNT14 MUTATED GALNT14 WILD-TYPE 
               20               460 
[1] "FLT4 MUTATION ANALYSIS"
[1] 3
  FLT4 MUTATED FLT4 WILD-TYPE 
            18            462 
  FLT4 MUTATED FLT4 WILD-TYPE 
            18            462 
[1] "ACBD5 MUTATION ANALYSIS"
[1] 3
  ACBD5 MUTATED ACBD5 WILD-TYPE 
             11             469 
  ACBD5 MUTATED ACBD5 WILD-TYPE 
             11             469 
[1] "CARD6 MUTATION ANALYSIS"
[1] 3
  CARD6 MUTATED CARD6 WILD-TYPE 
             14             466 
  CARD6 MUTATED CARD6 WILD-TYPE 
             14             466 
[1] "ANKRD44 MUTATION ANALYSIS"
[1] 3
  ANKRD44 MUTATED ANKRD44 WILD-TYPE 
               18               462 
  ANKRD44 MUTATED ANKRD44 WILD-TYPE 
               18               462 
[1] "DPEP2 MUTATION ANALYSIS"
[1] 3
  DPEP2 MUTATED DPEP2 WILD-TYPE 
              7             473 
  DPEP2 MUTATED DPEP2 WILD-TYPE 
              7             473 
[1] "TCEAL5 MUTATION ANALYSIS"
[1] 3
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              13              467 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              13              467 
[1] "PTPRH MUTATION ANALYSIS"
[1] 3
  PTPRH MUTATED PTPRH WILD-TYPE 
             22             458 
  PTPRH MUTATED PTPRH WILD-TYPE 
             22             458 
[1] "LMTK3 MUTATION ANALYSIS"
[1] 3
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              7             473 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              7             473 
[1] "ADAR MUTATION ANALYSIS"
[1] 3
  ADAR MUTATED ADAR WILD-TYPE 
             9            471 
  ADAR MUTATED ADAR WILD-TYPE 
             9            471 
[1] "CLCN5 MUTATION ANALYSIS"
[1] 3
  CLCN5 MUTATED CLCN5 WILD-TYPE 
              9             471 
  CLCN5 MUTATED CLCN5 WILD-TYPE 
              9             471 
[1] "MECP2 MUTATION ANALYSIS"
[1] 3
  MECP2 MUTATED MECP2 WILD-TYPE 
              9             471 
  MECP2 MUTATED MECP2 WILD-TYPE 
              9             471 
[1] "IL22RA2 MUTATION ANALYSIS"
[1] 3
  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
                6               474 
  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
                6               474 
[1] "MYO1H MUTATION ANALYSIS"
[1] 3
  MYO1H MUTATED MYO1H WILD-TYPE 
             12             468 
  MYO1H MUTATED MYO1H WILD-TYPE 
             12             468 
[1] "SERGEF MUTATION ANALYSIS"
[1] 3
  SERGEF MUTATED SERGEF WILD-TYPE 
               9              471 
  SERGEF MUTATED SERGEF WILD-TYPE 
               9              471 
[1] "TRIP13 MUTATION ANALYSIS"
[1] 3
  TRIP13 MUTATED TRIP13 WILD-TYPE 
              11              469 
  TRIP13 MUTATED TRIP13 WILD-TYPE 
              11              469 
[1] "GPR174 MUTATION ANALYSIS"
[1] 3
  GPR174 MUTATED GPR174 WILD-TYPE 
              16              464 
  GPR174 MUTATED GPR174 WILD-TYPE 
              16              464 
[1] "VARS MUTATION ANALYSIS"
[1] 3
  VARS MUTATED VARS WILD-TYPE 
             9            471 
  VARS MUTATED VARS WILD-TYPE 
             9            471 
[1] "CSNK1E MUTATION ANALYSIS"
[1] 3
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               6              474 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               6              474 
[1] "ANKRD7 MUTATION ANALYSIS"
[1] 3
  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
              10              470 
  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
              10              470 
[1] "SLC34A1 MUTATION ANALYSIS"
[1] 3
  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
                9               471 
  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
                9               471 
[1] "MSN MUTATION ANALYSIS"
[1] 3
  MSN MUTATED MSN WILD-TYPE 
            8           472 
  MSN MUTATED MSN WILD-TYPE 
            8           472 
[1] "FXYD5 MUTATION ANALYSIS"
[1] 3
  FXYD5 MUTATED FXYD5 WILD-TYPE 
              6             474 
  FXYD5 MUTATED FXYD5 WILD-TYPE 
              6             474 
[1] "NXF5 MUTATION ANALYSIS"
[1] 3
  NXF5 MUTATED NXF5 WILD-TYPE 
            13            467 
  NXF5 MUTATED NXF5 WILD-TYPE 
            13            467 
[1] "CDK16 MUTATION ANALYSIS"
[1] 3
  CDK16 MUTATED CDK16 WILD-TYPE 
              5             475 
  CDK16 MUTATED CDK16 WILD-TYPE 
              5             475 
[1] "COL19A1 MUTATION ANALYSIS"
[1] 3
  COL19A1 MUTATED COL19A1 WILD-TYPE 
               39               441 
  COL19A1 MUTATED COL19A1 WILD-TYPE 
               39               441 
[1] "PTPRN MUTATION ANALYSIS"
[1] 3
  PTPRN MUTATED PTPRN WILD-TYPE 
             18             462 
  PTPRN MUTATED PTPRN WILD-TYPE 
             18             462 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             12             468 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             12             468 
[1] "SYTL1 MUTATION ANALYSIS"
[1] 3
  SYTL1 MUTATED SYTL1 WILD-TYPE 
              5             475 
  SYTL1 MUTATED SYTL1 WILD-TYPE 
              5             475 
[1] "PIK3C2B MUTATION ANALYSIS"
[1] 3
  PIK3C2B MUTATED PIK3C2B WILD-TYPE 
               19               461 
  PIK3C2B MUTATED PIK3C2B WILD-TYPE 
               19               461 
[1] "FTSJ1 MUTATION ANALYSIS"
[1] 3
  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
              7             473 
  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
              7             473 
[1] "IFNA6 MUTATION ANALYSIS"
[1] 3
  IFNA6 MUTATED IFNA6 WILD-TYPE 
              6             474 
  IFNA6 MUTATED IFNA6 WILD-TYPE 
              6             474 
[1] "MME MUTATION ANALYSIS"
[1] 3
  MME MUTATED MME WILD-TYPE 
           14           466 
  MME MUTATED MME WILD-TYPE 
           14           466 
[1] "HYDIN MUTATION ANALYSIS"
[1] 3
  HYDIN MUTATED HYDIN WILD-TYPE 
             49             431 
  HYDIN MUTATED HYDIN WILD-TYPE 
             49             431 
[1] "ILF3 MUTATION ANALYSIS"
[1] 3
  ILF3 MUTATED ILF3 WILD-TYPE 
             5            475 
  ILF3 MUTATED ILF3 WILD-TYPE 
             5            475 
[1] "METTL2B MUTATION ANALYSIS"
[1] 3
  METTL2B MUTATED METTL2B WILD-TYPE 
                4               476 
  METTL2B MUTATED METTL2B WILD-TYPE 
                4               476 
[1] "ZNF511 MUTATION ANALYSIS"
[1] 3
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               9              471 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               9              471 
[1] "U2AF1L4 MUTATION ANALYSIS"
[1] 3
  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
                5               475 
  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
                5               475 
[1] "HTR3D MUTATION ANALYSIS"
[1] 3
  HTR3D MUTATED HTR3D WILD-TYPE 
              4             476 
  HTR3D MUTATED HTR3D WILD-TYPE 
              4             476 
[1] "EIF4E2 MUTATION ANALYSIS"
[1] 3
  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
               4              476 
  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
               4              476 
[1] "GAL3ST4 MUTATION ANALYSIS"
[1] 3
  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
               11               469 
  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
               11               469 
[1] "MBD1 MUTATION ANALYSIS"
[1] 3
  MBD1 MUTATED MBD1 WILD-TYPE 
            10            470 
  MBD1 MUTATED MBD1 WILD-TYPE 
            10            470 
[1] "WAC MUTATION ANALYSIS"
[1] 3
  WAC MUTATED WAC WILD-TYPE 
           11           469 
  WAC MUTATED WAC WILD-TYPE 
           11           469 
[1] "PGBD1 MUTATION ANALYSIS"
[1] 3
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             17             463 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             17             463 
[1] "GRHL2 MUTATION ANALYSIS"
[1] 3
  GRHL2 MUTATED GRHL2 WILD-TYPE 
              9             471 
  GRHL2 MUTATED GRHL2 WILD-TYPE 
              9             471 
[1] "TARS2 MUTATION ANALYSIS"
[1] 3
  TARS2 MUTATED TARS2 WILD-TYPE 
             10             470 
  TARS2 MUTATED TARS2 WILD-TYPE 
             10             470 
[1] "ARHGEF10L MUTATION ANALYSIS"
[1] 3
  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE 
                  8                 472 
  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE 
                  8                 472 
[1] "EIF4G3 MUTATION ANALYSIS"
[1] 3
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              13              467 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              13              467 
[1] "CRTC3 MUTATION ANALYSIS"
[1] 3
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              3             477 
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              3             477 
[1] "COL5A3 MUTATION ANALYSIS"
[1] 3
  COL5A3 MUTATED COL5A3 WILD-TYPE 
              20              460 
  COL5A3 MUTATED COL5A3 WILD-TYPE 
              20              460 
[1] "SF1 MUTATION ANALYSIS"
[1] 3
  SF1 MUTATED SF1 WILD-TYPE 
           12           468 
  SF1 MUTATED SF1 WILD-TYPE 
           12           468 
[1] "ZCCHC11 MUTATION ANALYSIS"
[1] 3
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               12               468 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               12               468 
[1] "AIFM1 MUTATION ANALYSIS"
[1] 3
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             13             467 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             13             467 
[1] "DCAF8 MUTATION ANALYSIS"
[1] 3
  DCAF8 MUTATED DCAF8 WILD-TYPE 
             12             468 
  DCAF8 MUTATED DCAF8 WILD-TYPE 
             12             468 
[1] "PPP2R2A MUTATION ANALYSIS"
[1] 3
  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
                6               474 
  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
                6               474 
[1] "IRF6 MUTATION ANALYSIS"
[1] 3
  IRF6 MUTATED IRF6 WILD-TYPE 
             9            471 
  IRF6 MUTATED IRF6 WILD-TYPE 
             9            471 
[1] "SIRPA MUTATION ANALYSIS"
[1] 3
  SIRPA MUTATED SIRPA WILD-TYPE 
             10             470 
  SIRPA MUTATED SIRPA WILD-TYPE 
             10             470 
[1] "ANGPT4 MUTATION ANALYSIS"
[1] 3
  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
              11              469 
  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
              11              469 
[1] "C12ORF71 MUTATION ANALYSIS"
[1] 3
  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
                 8                472 
  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
                 8                472 
[1] "CAPG MUTATION ANALYSIS"
[1] 3
  CAPG MUTATED CAPG WILD-TYPE 
             6            474 
  CAPG MUTATED CAPG WILD-TYPE 
             6            474 
[1] "PCDHGA6 MUTATION ANALYSIS"
[1] 3
  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE 
               26               454 
  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE 
               26               454 
[1] "ALPP MUTATION ANALYSIS"
[1] 3
  ALPP MUTATED ALPP WILD-TYPE 
            11            469 
  ALPP MUTATED ALPP WILD-TYPE 
            11            469 
[1] "ADCY6 MUTATION ANALYSIS"
[1] 3
  ADCY6 MUTATED ADCY6 WILD-TYPE 
              5             475 
  ADCY6 MUTATED ADCY6 WILD-TYPE 
              5             475 
[1] "GOLGA6B MUTATION ANALYSIS"
[1] 3
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
               10               470 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
               10               470 
[1] "TMEM135 MUTATION ANALYSIS"
[1] 3
  TMEM135 MUTATED TMEM135 WILD-TYPE 
                9               471 
  TMEM135 MUTATED TMEM135 WILD-TYPE 
                9               471 
[1] "MSR1 MUTATION ANALYSIS"
[1] 3
  MSR1 MUTATED MSR1 WILD-TYPE 
             7            473 
  MSR1 MUTATED MSR1 WILD-TYPE 
             7            473 
[1] "ZNF768 MUTATION ANALYSIS"
[1] 3
  ZNF768 MUTATED ZNF768 WILD-TYPE 
               8              472 
  ZNF768 MUTATED ZNF768 WILD-TYPE 
               8              472 
[1] "UNC93A MUTATION ANALYSIS"
[1] 3
  UNC93A MUTATED UNC93A WILD-TYPE 
               9              471 
  UNC93A MUTATED UNC93A WILD-TYPE 
               9              471 
[1] "CACNA2D4 MUTATION ANALYSIS"
[1] 3
  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE 
                23                457 
  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE 
                23                457 
[1] "KIRREL MUTATION ANALYSIS"
[1] 3
  KIRREL MUTATED KIRREL WILD-TYPE 
              16              464 
  KIRREL MUTATED KIRREL WILD-TYPE 
              16              464 
[1] "ZBTB5 MUTATION ANALYSIS"
[1] 3
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              3             477 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              3             477 
[1] "FANCM MUTATION ANALYSIS"
[1] 3
  FANCM MUTATED FANCM WILD-TYPE 
             31             449 
  FANCM MUTATED FANCM WILD-TYPE 
             31             449 
[1] "MYOF MUTATION ANALYSIS"
[1] 3
  MYOF MUTATED MYOF WILD-TYPE 
            16            464 
  MYOF MUTATED MYOF WILD-TYPE 
            16            464 
[1] "HNRNPA3 MUTATION ANALYSIS"
[1] 3
  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
                7               473 
  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
                7               473 
[1] "LRRFIP2 MUTATION ANALYSIS"
[1] 3
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                7               473 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                7               473 
[1] "MYLK MUTATION ANALYSIS"
[1] 3
  MYLK MUTATED MYLK WILD-TYPE 
            21            459 
  MYLK MUTATED MYLK WILD-TYPE 
            21            459 
[1] "AMELX MUTATION ANALYSIS"
[1] 3
  AMELX MUTATED AMELX WILD-TYPE 
             10             470 
  AMELX MUTATED AMELX WILD-TYPE 
             10             470 
[1] "TMEM145 MUTATION ANALYSIS"
[1] 3
  TMEM145 MUTATED TMEM145 WILD-TYPE 
               11               469 
  TMEM145 MUTATED TMEM145 WILD-TYPE 
               11               469 
[1] "GCDH MUTATION ANALYSIS"
[1] 3
  GCDH MUTATED GCDH WILD-TYPE 
             4            476 
  GCDH MUTATED GCDH WILD-TYPE 
             4            476 
[1] "CACNA2D1 MUTATION ANALYSIS"
[1] 3
  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
                40                440 
  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
                40                440 
[1] "OR52E8 MUTATION ANALYSIS"
[1] 3
  OR52E8 MUTATED OR52E8 WILD-TYPE 
              15              465 
  OR52E8 MUTATED OR52E8 WILD-TYPE 
              15              465 
[1] "ITGA2B MUTATION ANALYSIS"
[1] 3
  ITGA2B MUTATED ITGA2B WILD-TYPE 
              12              468 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
              12              468 
[1] "GKN1 MUTATION ANALYSIS"
[1] 3
  GKN1 MUTATED GKN1 WILD-TYPE 
             5            475 
  GKN1 MUTATED GKN1 WILD-TYPE 
             5            475 
[1] "ADAM11 MUTATION ANALYSIS"
[1] 3
  ADAM11 MUTATED ADAM11 WILD-TYPE 
              12              468 
  ADAM11 MUTATED ADAM11 WILD-TYPE 
              12              468 
[1] "FZD10 MUTATION ANALYSIS"
[1] 3
  FZD10 MUTATED FZD10 WILD-TYPE 
             28             452 
  FZD10 MUTATED FZD10 WILD-TYPE 
             28             452 
[1] "TEC MUTATION ANALYSIS"
[1] 3
  TEC MUTATED TEC WILD-TYPE 
           11           469 
  TEC MUTATED TEC WILD-TYPE 
           11           469 
[1] "MARCH6 MUTATION ANALYSIS"
[1] 3
  MARCH6 MUTATED MARCH6 WILD-TYPE 
              13              467 
  MARCH6 MUTATED MARCH6 WILD-TYPE 
              13              467 
[1] "AIFM3 MUTATION ANALYSIS"
[1] 3
  AIFM3 MUTATED AIFM3 WILD-TYPE 
              6             474 
  AIFM3 MUTATED AIFM3 WILD-TYPE 
              6             474 
[1] "MSRB2 MUTATION ANALYSIS"
[1] 3
  MSRB2 MUTATED MSRB2 WILD-TYPE 
              6             474 
  MSRB2 MUTATED MSRB2 WILD-TYPE 
              6             474 
[1] "KDM3B MUTATION ANALYSIS"
[1] 3
  KDM3B MUTATED KDM3B WILD-TYPE 
             14             466 
  KDM3B MUTATED KDM3B WILD-TYPE 
             14             466 
[1] "THPO MUTATION ANALYSIS"
[1] 3
  THPO MUTATED THPO WILD-TYPE 
             8            472 
  THPO MUTATED THPO WILD-TYPE 
             8            472 
[1] "CACNA1F MUTATION ANALYSIS"
[1] 3
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               27               453 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               27               453 
[1] "SELE MUTATION ANALYSIS"
[1] 3
  SELE MUTATED SELE WILD-TYPE 
            12            468 
  SELE MUTATED SELE WILD-TYPE 
            12            468 
[1] "THY1 MUTATION ANALYSIS"
[1] 3
  THY1 MUTATED THY1 WILD-TYPE 
             5            475 
  THY1 MUTATED THY1 WILD-TYPE 
             5            475 
[1] "TTK MUTATION ANALYSIS"
[1] 3
  TTK MUTATED TTK WILD-TYPE 
           18           462 
  TTK MUTATED TTK WILD-TYPE 
           18           462 
[1] "GGNBP2 MUTATION ANALYSIS"
[1] 3
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              11              469 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              11              469 
[1] "ADAM23 MUTATION ANALYSIS"
[1] 3
  ADAM23 MUTATED ADAM23 WILD-TYPE 
              27              453 
  ADAM23 MUTATED ADAM23 WILD-TYPE 
              27              453 
[1] "CHD8 MUTATION ANALYSIS"
[1] 3
  CHD8 MUTATED CHD8 WILD-TYPE 
            24            456 
  CHD8 MUTATED CHD8 WILD-TYPE 
            24            456 
[1] "TBC1D14 MUTATION ANALYSIS"
[1] 3
  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
                8               472 
  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
                8               472 
[1] "GPR128 MUTATION ANALYSIS"
[1] 3
  GPR128 MUTATED GPR128 WILD-TYPE 
              17              463 
  GPR128 MUTATED GPR128 WILD-TYPE 
              17              463 
[1] "RPL6 MUTATION ANALYSIS"
[1] 3
  RPL6 MUTATED RPL6 WILD-TYPE 
             3            477 
  RPL6 MUTATED RPL6 WILD-TYPE 
             3            477 
[1] "FRZB MUTATION ANALYSIS"
[1] 3
  FRZB MUTATED FRZB WILD-TYPE 
             9            471 
  FRZB MUTATED FRZB WILD-TYPE 
             9            471 
[1] "USP34 MUTATION ANALYSIS"
[1] 3
  USP34 MUTATED USP34 WILD-TYPE 
             23             457 
  USP34 MUTATED USP34 WILD-TYPE 
             23             457 
[1] "LCK MUTATION ANALYSIS"
[1] 3
  LCK MUTATED LCK WILD-TYPE 
           12           468 
  LCK MUTATED LCK WILD-TYPE 
           12           468 
[1] "FN1 MUTATION ANALYSIS"
[1] 3
  FN1 MUTATED FN1 WILD-TYPE 
           21           459 
  FN1 MUTATED FN1 WILD-TYPE 
           21           459 
[1] "RUFY2 MUTATION ANALYSIS"
[1] 3
  RUFY2 MUTATED RUFY2 WILD-TYPE 
              8             472 
  RUFY2 MUTATED RUFY2 WILD-TYPE 
              8             472 
[1] "YIPF1 MUTATION ANALYSIS"
[1] 3
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              3             477 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              3             477 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "COMPLETENESS_OF_RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCH_NUMBER"                          

Input Data has 23 rows and 480 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=134,	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=300,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=91,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=25,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 480 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY_PERFORMANCE_SCORE"           
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "NUMBER_PACK_YEARS_SMOKED"              
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[12] "COMPLETENESS_OF_RESECTION"             
[13] "RACE"                                  
[14] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=49, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
155 261  43  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
155 261  43  18 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
155 261  43  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
155 261  43  18 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
307  89  70   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  307    89    72 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
307  89  70   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  307    89    72 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=11, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=91, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=57, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
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   167  79
  TP53 WILD-TYPE 148  62
  TP53 MUTATED TP53 WILD-TYPE 
           246            210 
  TP53 MUTATED TP53 WILD-TYPE 
            79             62 
$`TP53 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       19.96        14.01         0.00         9.96        24.03        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 
        8.02        20.05         2.99        29.98        30.02        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4629 
       22.03         7.40         5.98         8.68        97.74        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-3396 TCGA-44-3918 
       35.28        44.61        14.73        46.98        37.15        34.06 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 
       33.30        28.37        12.59        23.77        10.78        27.78 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       21.63        23.18        32.45        61.28        16.44        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 
       12.03         7.17        36.07        18.87        29.00        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 
        8.55        15.98        11.54        13.64        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4514 TCGA-49-6767 TCGA-50-5045 
       28.57        12.66        14.07        55.89        22.26        71.47 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       70.55        31.04        49.28         9.27        14.27        78.67 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       15.12        18.64        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8460 
       25.55        11.05        12.16         6.21         0.72        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6712 
       34.29        30.54         9.21        23.05         2.86         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6975 TCGA-55-6979 TCGA-55-6985 TCGA-55-7227 
       42.51        40.73         3.88         7.79        40.54         1.74 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1.15         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.28         1.12        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
        6.15        19.82         0.16        29.72         3.29         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        0.13        23.64         1.08        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
        0.76         0.36         0.26        17.72         0.30         6.64 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       21.40        20.58         0.92        20.19        19.99         4.57 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A46Y 
       88.64        49.25        47.80        56.71        67.96        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5775 TCGA-64-5778 TCGA-67-3771 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 
        2.04        42.90        20.05         6.64         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-8520 
        2.30         2.93        12.56         4.24         7.04         0.10 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
       26.30         4.31         5.39        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 
        5.69        19.27        35.93        21.90        19.50        38.50 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       26.53        31.20         8.02        39.35        10.55       214.62 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09         5.88        31.13        34.39 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.43        19.89         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8672 
       15.75        15.85        23.05        21.47         1.15         0.62 
TCGA-86-8673 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6831 TCGA-91-6836 
       14.96        17.62        13.64        41.36        10.19        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 
       12.23        27.68         7.36         1.18         1.45         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 
       18.67        12.39        15.68        27.29         2.76        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
       25.48         5.95         0.59        17.92        18.12        14.30 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 
       21.60        20.19        21.44        19.76        24.56        34.85 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 
       36.76         5.59        18.08        19.00         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA 
       38.63         2.76        86.14        86.04        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J 
        2.43        11.05        14.10        19.13        71.05        59.11 

$`TP53 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 TCGA-05-4417 
       50.07         3.98        45.01        37.02        19.00        14.96 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 
        9.01        12.00        21.99        15.02        15.02         9.04 
TCGA-05-5715 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-7271 
        2.04       120.79        37.71        49.05        11.64        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3398 TCGA-44-3919 
        4.37        13.15        24.36        42.77        38.24         6.25 
TCGA-44-4112 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-7659 TCGA-44-7671 
       26.56         9.93        23.15        63.72        14.60        17.59 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-49-4486 
       23.64         3.25        15.32         9.44        11.08        76.21 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        46.72        32.84         8.81        29.46        29.75 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       14.63        12.13        29.26        17.16        11.64        20.52 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 
       15.72        60.16         8.22        40.60        21.47         8.45 
TCGA-50-5942 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-53-7813 
       29.03        41.69        10.13        25.61         7.59        13.94 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       48.62         0.07        32.65        15.25         0.82        48.49 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7725 TCGA-55-7728 
      107.21        70.26         0.59         7.99         1.28         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 
        1.78         1.45        15.19        19.66        19.73        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 
       17.98         1.51         2.17         0.95         0.49         0.10 
TCGA-55-8513 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 
        4.80         0.49        20.71         1.58        19.59        15.81 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46V 
       39.98        42.38        14.60        19.53        54.35        72.30 
TCGA-62-A470 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
       39.25        87.98        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 
       14.04         5.72         4.64        13.87         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 
       13.61         7.56        14.01        13.45         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 
       23.38        29.98        15.35         1.32         1.25        39.09 
TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       20.58        39.52        24.99        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-86-6562 
       53.33        10.75        32.68        39.75        77.59        12.36 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8076 TCGA-86-8278 
       13.87        20.55        16.70        24.49        16.08        15.65 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 
       14.60        13.91        30.84        27.58        13.32        13.32 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6849 TCGA-91-7771 
       26.47        10.62         1.97         2.60         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JQ 
       16.60        14.27        19.82         9.76         4.18        17.29 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       15.65        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
       63.52         0.72        18.67         5.39        15.39        16.41 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       20.58        20.52        17.75        20.84        18.67        20.68 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
        1.45        24.30        23.80        35.47        16.44        14.30 
TCGA-L9-A443 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
        3.81        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG 
        5.29        10.09        29.46        14.66        73.91        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 

  TP53 MUTATED TP53 WILD-TYPE 
          0.00           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        214.62         223.96 
  TP53 MUTATED TP53 WILD-TYPE 
         18.64          17.44 
[1] "0.0 - 214.6 (18.6)" "0.1 - 224.0 (17.4)"
[1] "hr=" "1.2"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TP53 MUTATED         3       61       73        24        35         36
  TP53 WILD-TYPE       1       62       60        22        32         34
                vv
clus             STAGE IIIB STAGE IV
  TP53 MUTATED            8       15
  TP53 WILD-TYPE          3       10
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               3              1
  STAGE IA             61             62
  STAGE IB             73             60
  STAGE IIA            24             22
  STAGE IIB            35             32
  STAGE IIIA           36             34
  STAGE IIIB            8              3
  STAGE IV             15             10
[1] 8 2
[1] TRUE
[1] "dimension of 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    79 142  20  12
  TP53 WILD-TYPE  76 119  23   6
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           79             76
  T2          142            119
  T3           20             23
  T4           12              6
[1] 4 2
[1] TRUE
[1] "dimension of 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   164  47    38
  TP53 WILD-TYPE 143  42    34
D1V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0             164            143
  N1              47             42
  N2+N3           38             34
[1] 3 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   166  14
  TP53 WILD-TYPE 161   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    166   14
  TP53 WILD-TYPE  161    9
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          166            161
  1           14              9
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED   138 117
  TP53 WILD-TYPE 121 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    138  117
  TP53 WILD-TYPE  121  104
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE          138            121
  MALE            117            104
[1] 2 2
[1] FALSE
D1V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TP53 MUTATED                            8                                52
  TP53 WILD-TYPE                         10                                50
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                  171
  TP53 WILD-TYPE                                                123
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TP53 MUTATED                                            1
  TP53 WILD-TYPE                                          3
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TP53 MUTATED                                              11
  TP53 WILD-TYPE                                             8
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  TP53 MUTATED                                0
  TP53 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  TP53 MUTATED                                    1
  TP53 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TP53 MUTATED                              0                             7
  TP53 WILD-TYPE                            2                            15
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TP53 MUTATED                                               3
  TP53 WILD-TYPE                                             2
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  TP53 MUTATED                              1
  TP53 WILD-TYPE                            8
D1V9, multiclass
                                                    clus
vv                                                   TP53 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          171
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                11
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 7
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 3
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   TP53 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            123
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  15
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   2
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                cls
clus               0   1
  TP53 MUTATED    13 242
  TP53 WILD-TYPE   7 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     13  242
  TP53 WILD-TYPE    7  218
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            13              7
  YES          242            218
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, continuous
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   163   5   1  14
  TP53 WILD-TYPE 147   6   3  11
D1V13, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          163            147
  R1            5              6
  R2            1              3
  RX           14             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     3
  TP53 WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          22   197
  TP53 WILD-TYPE                         7   180
D1V14, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                  22              7
  WHITE                                     197            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"
D1V15, binary
                cls
clus               0   1
  TP53 MUTATED     6 188
  TP53 WILD-TYPE   0 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6  188
  TP53 WILD-TYPE    0  161
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                6              0
  NOT HISPANIC OR LATINO          188            161
[1] 2 2
[1] FALSE

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  KRAS MUTATED   100  43
  KRAS WILD-TYPE 215  98
  KRAS MUTATED KRAS WILD-TYPE 
           143            313 
  KRAS MUTATED KRAS WILD-TYPE 
            43             98 
$`KRAS MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 
       50.07         3.98        37.02         0.00        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4427 TCGA-05-4433 TCGA-38-4626 TCGA-44-6145 
       14.96         9.01        26.01        24.00       120.79        10.78 
TCGA-44-6146 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 
        9.93        63.72        32.45        14.60        12.03        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47F TCGA-49-4505 TCGA-49-4510 
       23.64        12.66        15.32        11.08        14.07        29.46 
TCGA-49-6761 TCGA-50-5051 TCGA-50-5932 TCGA-50-5941 TCGA-50-8457 TCGA-50-8459 
       11.64        15.72        40.60        18.64        25.61         7.59 
TCGA-53-7813 TCGA-55-1595 TCGA-55-6642 TCGA-55-6970 TCGA-55-6975 TCGA-55-6983 
       13.94        48.62        32.65        15.25         3.88        60.03 
TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7725 
       24.99         0.59         1.15         7.99         1.32         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.28         0.79         1.78         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 
        6.15        19.66         0.13        15.65        17.98         2.17 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 
       15.42         0.76         0.49         0.10         6.64         0.49 
TCGA-55-8616 TCGA-55-A490 TCGA-55-A494 TCGA-62-8398 TCGA-62-A46R TCGA-62-A46S 
        1.58         1.58        15.81        14.60        56.71        54.35 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 TCGA-69-7973 
       87.98         2.04        42.90        28.47        14.04         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4659 
        6.05         2.30        12.56        14.01        13.45        23.38 
TCGA-73-4662 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-78-7145 TCGA-78-7148 
       29.98         4.31         1.25        39.09        27.16        20.58 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 TCGA-78-7539 TCGA-78-7540 
       22.29         7.07         8.48        88.14        10.75        39.35 
TCGA-78-8655 TCGA-83-5908 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 
       77.59        27.09        13.87        19.43        24.49         4.57 
TCGA-86-8076 TCGA-86-8359 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-91-6828 
       16.08        14.60        13.32        13.32        17.62        10.62 
TCGA-91-6836 TCGA-91-8497 TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-95-7039 
       13.71        14.27         9.76         6.12         1.08         1.12 
TCGA-95-7562 TCGA-95-7567 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 
        2.86        18.67        21.40        18.18        19.89        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M0 TCGA-97-A4M5 
        0.59         0.72        15.39        14.30        21.44        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
       24.56        34.85        36.76         1.45         5.59        23.80 
TCGA-J2-A4AG TCGA-L9-A443 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T7 
       16.44         3.81         2.76        49.35        86.04         5.49 
TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        5.29        10.09        29.46        11.05        14.10        19.13 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.43        19.82 

$`KRAS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       19.96        14.01        45.01         9.96        24.03        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        8.02        20.05        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        25.02        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        8.68        97.74        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
       27.78        23.15        21.63        23.18        61.28        16.44 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 
       19.46         7.17        36.07        18.87        29.00         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.98         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       32.84         8.81        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       29.26        17.16        22.26        20.52        71.47        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47         8.45        15.12        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
        6.21        41.69         0.72        10.13        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       30.54         9.21        23.05         2.86         0.07         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       42.51        40.73         0.82        48.49         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        2.20        45.34        32.71        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7727 
        1.74         0.20         0.13         3.12        23.18         1.12 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        1.45        18.64        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
        3.29        19.73         5.06        23.64         1.08         1.51 
TCGA-55-8208 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
       22.16         1.45         0.95         0.36         0.26        17.72 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        0.30         4.80        17.62         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40        20.58        19.59         0.92 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       20.19        19.99         4.57        39.98        42.38        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       49.25        47.80        19.53        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 
       38.37        28.41        51.25        20.05        18.84         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
        5.42         2.93         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       52.60        26.30        15.35         1.32         5.39        23.51 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10         5.69        19.27        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      104.19       223.96        26.53        31.20         8.02        53.33 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
       10.55        32.68       214.62        39.75        10.55       110.50 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
       12.36         5.88        31.13        34.39        20.55        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
       16.70         4.08        24.33         0.79        15.75        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        21.47         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       27.58         0.62        14.96        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.18        16.60         1.18         1.45        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7944 
        4.18        23.61        19.00        17.29         1.22        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 
       15.68        15.65        27.29         2.76        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       63.52        43.79         5.95        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       18.12        16.41        21.60        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD 
       20.52        17.75        18.67        20.68        24.30        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       35.47        19.00        14.30         0.20        27.19        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.14        58.45        37.35        58.85        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A 
        2.43        14.66        73.91        71.05        29.13         0.26 
TCGA-O1-A52J 
       59.11 

  KRAS MUTATED KRAS WILD-TYPE 
          0.00           0.07 
  KRAS MUTATED KRAS WILD-TYPE 
        120.79         223.96 
  KRAS MUTATED KRAS WILD-TYPE 
         14.10          19.96 
[1] "0.0 - 120.8 (14.1)" "0.1 - 224.0 (20.0)"
[1] "hr=" "1.3"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KRAS MUTATED         1       36       35        16        25         24
  KRAS WILD-TYPE       3       87       98        30        42         46
                vv
clus             STAGE IIIB STAGE IV
  KRAS MUTATED            3        9
  KRAS WILD-TYPE          8       16
D2V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               1              3
  STAGE IA             36             87
  STAGE IB             35             98
  STAGE IIA            16             30
  STAGE IIB            25             42
  STAGE IIIA           24             46
  STAGE IIIB            3              8
  STAGE IV              9             16
[1] 8 2
[1] TRUE
[1] "dimension of 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    42  82  17   8
  KRAS WILD-TYPE 113 179  26  10
D2V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1           42            113
  T2           82            179
  T3           17             26
  T4            8             10
[1] 4 2
[1] TRUE
[1] "dimension of 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    94  30    23
  KRAS WILD-TYPE 213  59    49
D2V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  N0              94            213
  N1              30             59
  N2+N3           23             49
[1] 3 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
  KRAS MUTATED    97   9
  KRAS WILD-TYPE 230  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     97    9
  KRAS WILD-TYPE  230   14
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           97            230
  1            9             14
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  KRAS MUTATED    81  69
  KRAS WILD-TYPE 178 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     81   69
  KRAS WILD-TYPE  178  152
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           81            178
  MALE             69            152
[1] 2 2
[1] FALSE
D2V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KRAS MUTATED                            6                                33
  KRAS WILD-TYPE                         12                                69
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                   84
  KRAS WILD-TYPE                                                210
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KRAS MUTATED                                            1
  KRAS WILD-TYPE                                          3
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KRAS MUTATED                                               8
  KRAS WILD-TYPE                                            11
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  KRAS MUTATED                                1
  KRAS WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  KRAS MUTATED                                    0
  KRAS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KRAS MUTATED                              1                            10
  KRAS WILD-TYPE                            1                            12
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KRAS MUTATED                                               1
  KRAS WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  KRAS MUTATED                              5
  KRAS WILD-TYPE                            4
D2V9, multiclass
                                                    clus
vv                                                   KRAS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 8
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                10
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  5
                                                    clus
vv                                                   KRAS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  11
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                  12
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                cls
clus               0   1
  KRAS MUTATED     4 146
  KRAS WILD-TYPE  16 314
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4  146
  KRAS WILD-TYPE   16  314
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             4             16
  YES          146            314
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, continuous
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED    98   3   2   8
  KRAS WILD-TYPE 212   8   2  17
D2V13, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           98            212
  R1            3              8
  R2            2              2
  RX            8             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     3
  KRAS WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                          11   114
  KRAS WILD-TYPE                        18   263
D2V14, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                  11             18
  WHITE                                     114            263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                cls
clus               0   1
  KRAS MUTATED     0 108
  KRAS WILD-TYPE   6 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0  108
  KRAS WILD-TYPE    6  241
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO          108            241
[1] 2 2
[1] FALSE

Clustering(3) Variable = KEAP1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  KEAP1 MUTATED    50  30
  KEAP1 WILD-TYPE 265 111
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             80             376 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             30             111 
$`KEAP1 MUTATED`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4418 TCGA-35-5375 TCGA-38-4631 
       14.01        45.01         0.00         9.01         8.68        11.64 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       63.72        61.28        16.44        19.46        36.07        18.87 
TCGA-44-7671 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4506 
       17.59        11.08        13.64        76.21        28.57        32.84 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-50-5051 TCGA-50-5068 
        8.81        55.89        14.63        12.13        15.72        49.28 
TCGA-50-5936 TCGA-50-5939 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6970 
        8.45        15.12        34.29         9.21         2.86        15.25 
TCGA-55-6972 TCGA-55-6987 TCGA-55-7815 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 
       48.49        70.26         1.78         0.16        29.72         0.13 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8620 TCGA-55-A492 
        0.76         0.95         0.36        17.72         2.17        19.59 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-A46O TCGA-62-A470 TCGA-64-5781 TCGA-67-3771 
       20.19        14.60        47.80        39.25        51.25        20.05 
TCGA-69-8253 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       14.01        26.30         4.31         5.39         1.25        39.09 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        5.69        35.93        24.99        19.50        32.09         5.88 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7633 TCGA-86-8358 TCGA-86-8674 
      104.19         8.48        88.14        32.68        21.47        13.32 
TCGA-91-6848 TCGA-91-6849 TCGA-95-7043 TCGA-95-7947 TCGA-97-8176 TCGA-97-8179 
        7.36         1.15         1.22        15.68        15.39        14.30 
TCGA-97-A4M3 TCGA-99-8033 TCGA-J2-8194 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A5C7 
       17.75         5.59        23.80         5.49        29.46        73.91 
TCGA-NJ-A4YQ TCGA-NJ-A55R 
       29.13        19.82 

$`KEAP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4390 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        19.96        37.02         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       29.98        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
        9.93        27.78        23.15        21.63        23.18        32.45 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
       14.60        12.03         7.17        29.00        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       13.45        28.11        12.66        35.54        46.72        14.07 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       29.46        29.75        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
       20.52        71.47        70.55        60.16        31.04         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
        9.27        14.27        40.60        78.67        21.47        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
       25.61         7.59        27.25        30.54        13.94        23.05 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 
       32.71        60.03        24.99        40.54       107.21         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       19.82        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
       22.16        15.42         1.45         0.26         0.49         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       20.58         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       42.38        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       67.96        72.30        13.61        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.41        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
        7.56         6.05         2.30         2.93        12.56        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
       29.98        15.35         1.32        23.51       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7159 
       19.27        20.58        21.90        39.52        38.50        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
       22.29         7.07       223.96        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        10.75        39.35        10.55       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 
       17.29         1.12         2.86        18.67        12.39        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        0.72        18.67        17.92         5.39        18.12        16.41 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        24.30        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF 
        5.29        41.59        31.23         2.43        10.09        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        19.13        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        1.64         0.26         0.43        59.11 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
           0.00            0.07 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         104.19          223.96 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
          16.08           18.64 
[1] "0.0 - 104.2 (16.1)" "0.1 - 224.0 (18.6)"
[1] "hr=" "1.2"
D3V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KEAP1 MUTATED         0       25       17         6         9         15
  KEAP1 WILD-TYPE       4       98      116        40        58         55
                 vv
clus              STAGE IIIB STAGE IV
  KEAP1 MUTATED            3        9
  KEAP1 WILD-TYPE          8       16
D3V3, multiclass
            clus
vv           KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA              25              98
  STAGE IB              17             116
  STAGE IIA              6              40
  STAGE IIB              9              58
  STAGE IIIA            15              55
  STAGE IIIB             3               8
  STAGE IV               9              16
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KEAP1 MUTATED    29  43   7   4
  KEAP1 WILD-TYPE 126 218  36  14
D3V4, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  T1            29             126
  T2            43             218
  T3             7              36
  T4             4              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"
                 vv
clus               N0  N1 N2+N3
  KEAP1 MUTATED    51  16    15
  KEAP1 WILD-TYPE 256  73    57
D3V5, multiclass
       clus
vv      KEAP1 MUTATED KEAP1 WILD-TYPE
  N0               51             256
  N1               16              73
  N2+N3            15              57
[1] 3 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
  KEAP1 MUTATED    50   9
  KEAP1 WILD-TYPE 277  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     50    9
  KEAP1 WILD-TYPE  277   14
   clus
vv  KEAP1 MUTATED KEAP1 WILD-TYPE
  0            50             277
  1             9              14
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  KEAP1 MUTATED    36  48
  KEAP1 WILD-TYPE 223 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     36   48
  KEAP1 WILD-TYPE  223  173
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE            36             223
  MALE              48             173
[1] 2 2
[1] FALSE
D3V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KEAP1 MUTATED                            4                                20
  KEAP1 WILD-TYPE                         14                                82
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KEAP1 MUTATED                                                   50
  KEAP1 WILD-TYPE                                                244
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KEAP1 MUTATED                                            0
  KEAP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KEAP1 MUTATED                                               1
  KEAP1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KEAP1 MUTATED                                1
  KEAP1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KEAP1 MUTATED                                    0
  KEAP1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KEAP1 MUTATED                              0                             6
  KEAP1 WILD-TYPE                            2                            16
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KEAP1 MUTATED                                               0
  KEAP1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KEAP1 MUTATED                              2
  KEAP1 WILD-TYPE                            7
D3V9, multiclass
                                                    clus
vv                                                   KEAP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            50
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  6
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   2
                                                    clus
vv                                                   KEAP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             244
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   16
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                 cls
clus                0   1
  KEAP1 MUTATED     5  79
  KEAP1 WILD-TYPE  15 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      5   79
  KEAP1 WILD-TYPE   15  381
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO              5              15
  YES            79             381
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, continuous
                 vv
clus               R0  R1  R2  RX
  KEAP1 MUTATED    54   3   0   4
  KEAP1 WILD-TYPE 256   8   4  21
D3V13, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  R0            54             256
  R1             3               8
  R2             0               4
  RX             4              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KEAP1 MUTATED                                  0     0
  KEAP1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED                           6    69
  KEAP1 WILD-TYPE                        23   308
D3V14, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    6              23
  WHITE                                       69             308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                 cls
clus                0   1
  KEAP1 MUTATED     2  56
  KEAP1 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      2   56
  KEAP1 WILD-TYPE    4  293
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO            56             293
[1] 2 2
[1] FALSE

Clustering(4) Variable = EGFR MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    39  24
  EGFR WILD-TYPE 276 117
  EGFR MUTATED EGFR WILD-TYPE 
            63            393 
  EGFR MUTATED EGFR WILD-TYPE 
            24            117 
$`EGFR MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-5423 TCGA-05-5425 TCGA-38-4627 TCGA-38-4628 
       19.96         8.02         4.96        29.00        37.71        49.05 
TCGA-38-4629 TCGA-38-6178 TCGA-44-2661 TCGA-44-6147 TCGA-44-A4SU TCGA-49-4490 
       28.41        14.73        24.36        27.78        13.45        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-50-5066 TCGA-50-5944 TCGA-50-6591 TCGA-50-6595 
       35.54        46.72        31.04        25.12         3.91         6.21 
TCGA-50-6673 TCGA-55-6968 TCGA-55-6980 TCGA-55-6981 TCGA-55-7570 TCGA-55-7573 
        0.72        42.51         2.20        45.34         0.20         0.13 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8506 TCGA-55-A48Z TCGA-62-8394 TCGA-62-8402 
       23.64         1.51         0.36        21.40         4.57        49.25 
TCGA-62-A46U TCGA-64-1681 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 
       67.96        38.37        18.84        13.87         6.64         5.42 
TCGA-71-8520 TCGA-78-7147 TCGA-78-7155 TCGA-78-7158 TCGA-86-8055 TCGA-86-8074 
        0.10        19.27        38.50         5.88         4.08         0.79 
TCGA-86-8075 TCGA-86-8280 TCGA-86-8668 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6835 
       15.75        23.05        13.91        17.62        13.64         2.60 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7947 TCGA-97-8171 TCGA-97-8172 TCGA-97-8177 
       19.00         1.12        15.68        18.67        17.92        16.41 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-J2-8192 
       21.60        20.58        19.76        18.67        20.68        24.30 
TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T9 
       58.45        58.85        41.59 

$`EGFR WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       15.02        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        8.68        97.74       120.79        35.28        11.64        44.61 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        46.98        13.15        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
       12.59        23.77        10.78         9.93        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       28.11        28.57        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 
       22.55        42.35        25.55        11.05        12.16        41.69 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65         0.79        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88         5.49         7.79        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.99         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.08         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O 
       19.99        39.98        42.38        14.60        88.64        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 
       40.96        29.92        56.81        20.65        55.43        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
       14.04         5.72         4.64         6.12        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
       13.45         4.24         7.04         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       32.09        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
       16.70        24.49         4.57        24.33        16.08        15.65 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
       15.85        21.47        14.60         1.15        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6828 
        0.62        14.96        13.32        13.32        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
        1.08        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
        0.59         0.72         5.39        18.12        15.39        14.30 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 
       20.19        21.44        20.52        17.75        20.84        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85        36.76         1.45         5.59        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19        38.63         2.76        86.14        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       86.04         5.49         5.29        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  EGFR MUTATED EGFR WILD-TYPE 
           0.1            0.0 
  EGFR MUTATED EGFR WILD-TYPE 
         67.96         223.96 
  EGFR MUTATED EGFR WILD-TYPE 
         18.67          17.75 
[1] "0.1 - 68.0 (18.7)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.5"
D4V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  EGFR MUTATED         2       15       13         7        11         10
  EGFR WILD-TYPE       2      108      120        39        56         60
                vv
clus             STAGE IIIB STAGE IV
  EGFR MUTATED            3        6
  EGFR WILD-TYPE          8       19
D4V3, multiclass
            clus
vv           EGFR MUTATED EGFR WILD-TYPE
  STAGE I               2              2
  STAGE IA             15            108
  STAGE IB             13            120
  STAGE IIA             7             39
  STAGE IIB            11             56
  STAGE IIIA           10             60
  STAGE IIIB            3              8
  STAGE IV              6             19
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGFR MUTATED    23  33   7   3
  EGFR WILD-TYPE 132 228  36  15
D4V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1           23            132
  T2           33            228
  T3            7             36
  T4            3             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"
                vv
clus              N0  N1 N2+N3
  EGFR MUTATED    38  12    14
  EGFR WILD-TYPE 269  77    58
D4V5, multiclass
       clus
vv      EGFR MUTATED EGFR WILD-TYPE
  N0              38            269
  N1              12             77
  N2+N3           14             58
[1] 3 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
  EGFR MUTATED    48   5
  EGFR WILD-TYPE 279  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     48    5
  EGFR WILD-TYPE  279   18
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0           48            279
  1            5             18
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus               0   1
  EGFR MUTATED    44  23
  EGFR WILD-TYPE 215 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     44   23
  EGFR WILD-TYPE  215  198
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           44            215
  MALE             23            198
[1] 2 2
[1] FALSE
D4V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EGFR MUTATED                            3                                19
  EGFR WILD-TYPE                         15                                83
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EGFR MUTATED                                                   38
  EGFR WILD-TYPE                                                256
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  EGFR MUTATED                                            1
  EGFR WILD-TYPE                                          3
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  EGFR MUTATED                                               3
  EGFR WILD-TYPE                                            16
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  EGFR MUTATED                                0
  EGFR WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  EGFR MUTATED                                    1
  EGFR WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  EGFR MUTATED                              0                             2
  EGFR WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  EGFR MUTATED                                               0
  EGFR WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  EGFR MUTATED                              0
  EGFR WILD-TYPE                            9
D4V9, multiclass
                                                    clus
vv                                                   EGFR MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           38
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   EGFR WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            256
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                cls
clus               0   1
  EGFR MUTATED     0  67
  EGFR WILD-TYPE  20 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   67
  EGFR WILD-TYPE   20  393
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO             0             20
  YES           67            393
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, continuous
                vv
clus              R0  R1  R2  RX
  EGFR MUTATED    42   2   1   3
  EGFR WILD-TYPE 268   9   3  22
D4V13, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  R0           42            268
  R1            2              9
  R2            1              3
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     3
  EGFR WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           3    52
  EGFR WILD-TYPE                        26   325
D4V14, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                   3             26
  WHITE                                      52            325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                cls
clus               0   1
  EGFR MUTATED     0  51
  EGFR WILD-TYPE   6 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   51
  EGFR WILD-TYPE    6  298
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           51            298
[1] 2 2
[1] FALSE

Clustering(5) Variable = RBM10 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED    21  11
  RBM10 WILD-TYPE 294 130
  RBM10 MUTATED RBM10 WILD-TYPE 
             32             424 
  RBM10 MUTATED RBM10 WILD-TYPE 
             11             130 
$`RBM10 MUTATED`
TCGA-05-4395 TCGA-05-4403 TCGA-05-4418 TCGA-05-4424 TCGA-44-7659 TCGA-44-7661 
        0.00        19.00         9.01        30.02        14.60        12.03 
TCGA-44-A47A TCGA-49-4494 TCGA-55-6983 TCGA-55-7281 TCGA-55-7727 TCGA-55-7815 
       15.32        35.54        60.03         0.59         1.12         1.78 
TCGA-55-8090 TCGA-55-8205 TCGA-55-8208 TCGA-55-8620 TCGA-55-A490 TCGA-55-A491 
       19.66         1.08        22.16         2.17         1.58        20.58 
TCGA-62-A472 TCGA-64-1676 TCGA-64-5775 TCGA-69-8254 TCGA-73-7498 TCGA-78-7148 
       29.92        56.81         2.04        13.45        39.09        20.58 
TCGA-78-7158 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-91-6828 TCGA-91-6848 
        5.88         8.48        26.53        53.33        10.62         7.36 
TCGA-97-A4M7 TCGA-MP-A4SW 
       20.68        58.45 

$`RBM10 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05         8.02        20.05         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       14.96        29.98        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       23.18        63.72        32.45        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25         8.55        15.98         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 
       24.99        40.54       107.21        70.26         1.74         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         1.28         0.79         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
       15.65        17.98         1.51         2.17        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       39.25        40.96        20.65        55.43        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        2.93        12.56        14.01         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 
        4.31         1.32         5.39         1.25        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        19.27        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        38.50        32.09        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        7.07       104.19       223.96        88.14        31.20         8.02 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63         2.76        86.14        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.00            0.07 
  RBM10 MUTATED RBM10 WILD-TYPE 
          60.03          223.96 
  RBM10 MUTATED RBM10 WILD-TYPE 
          14.96           18.10 
[1] "0.0 - 60.0 (15.0)"  "0.1 - 224.0 (18.1)"
[1] "hr=" "1.3"
D5V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RBM10 MUTATED         0        9        5         1         7          7
  RBM10 WILD-TYPE       4      114      128        45        60         63
                 vv
clus              STAGE IIIB STAGE IV
  RBM10 MUTATED            2        1
  RBM10 WILD-TYPE          9       24
D5V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                0               4
  STAGE IA               9             114
  STAGE IB               5             128
  STAGE IIA              1              45
  STAGE IIB              7              60
  STAGE IIIA             7              63
  STAGE IIIB             2               9
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM10 MUTATED    11  15   4   3
  RBM10 WILD-TYPE 144 246  39  15
D5V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1            11             144
  T2            15             246
  T3             4              39
  T4             3              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"
                 vv
clus               N0  N1 N2+N3
  RBM10 MUTATED    19   5     8
  RBM10 WILD-TYPE 288  84    64
D5V5, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  N0               19             288
  N1                5              84
  N2+N3             8              64
[1] 3 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
  RBM10 MUTATED    24   1
  RBM10 WILD-TYPE 303  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     24    1
  RBM10 WILD-TYPE  303   22
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0            24             303
  1             1              22
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  RBM10 MUTATED    10  23
  RBM10 WILD-TYPE 249 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     10   23
  RBM10 WILD-TYPE  249  198
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE            10             249
  MALE              23             198
[1] 2 2
[1] FALSE
D5V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RBM10 MUTATED                            0                                10
  RBM10 WILD-TYPE                         18                                92
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RBM10 MUTATED                                                   21
  RBM10 WILD-TYPE                                                273
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RBM10 MUTATED                                            0
  RBM10 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RBM10 MUTATED                                               1
  RBM10 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RBM10 MUTATED                                0
  RBM10 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RBM10 MUTATED                                    0
  RBM10 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RBM10 MUTATED                              0                             0
  RBM10 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RBM10 MUTATED                                               0
  RBM10 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RBM10 MUTATED                              1
  RBM10 WILD-TYPE                            8
D5V9, multiclass
                                                    clus
vv                                                   RBM10 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            21
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   RBM10 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             273
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                 cls
clus                0   1
  RBM10 MUTATED     2  31
  RBM10 WILD-TYPE  18 429
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2   31
  RBM10 WILD-TYPE   18  429
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO              2              18
  YES            31             429
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, continuous
                 vv
clus               R0  R1  R2  RX
  RBM10 MUTATED    27   2   0   0
  RBM10 WILD-TYPE 283   9   4  25
D5V13, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0            27             283
  R1             2               9
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM10 MUTATED                                  0     0
  RBM10 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED                           0    26
  RBM10 WILD-TYPE                        29   351
D5V14, multiclass
                                  clus
vv                                 RBM10 MUTATED RBM10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       26             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                 cls
clus                0   1
  RBM10 MUTATED     0  20
  RBM10 WILD-TYPE   6 329
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0   20
  RBM10 WILD-TYPE    6  329
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            20             329
[1] 2 2
[1] FALSE

Clustering(6) Variable = SMARCA4 MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    22  14
  SMARCA4 WILD-TYPE 293 127
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               36               420 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               14               127 
$`SMARCA4 MUTATED`
TCGA-05-4432 TCGA-05-5420 TCGA-35-5375 TCGA-38-4631 TCGA-44-2656 TCGA-44-8117 
       25.02        15.02         8.68        11.64        46.98        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-49-6742 TCGA-49-6767 TCGA-50-5072 TCGA-50-5930 
        3.25        15.98        14.63        22.26         8.22         9.27 
TCGA-50-5936 TCGA-53-7624 TCGA-55-6543 TCGA-55-6969 TCGA-55-6975 TCGA-55-8089 
        8.45        34.29         0.07        40.73         3.88         3.29 
TCGA-55-A48Y TCGA-55-A48Z TCGA-62-A46O TCGA-67-3771 TCGA-69-7980 TCGA-69-8255 
       20.71        21.40        47.80        20.05        12.56         4.24 
TCGA-78-7148 TCGA-78-8640 TCGA-78-8660 TCGA-86-7711 TCGA-86-8585 TCGA-86-8674 
       20.58       214.62        10.55        34.39         1.15        13.32 
TCGA-97-8175 TCGA-97-8176 TCGA-J2-A4AD TCGA-MP-A4SY TCGA-MP-A4TA TCGA-NJ-A4YQ 
       18.12        15.39        18.08        49.35        31.23        29.13 

$`SMARCA4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
       23.64         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        12.13        29.26        17.16        11.64 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 
       49.28        14.27        40.60        78.67        21.47        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05        48.62         2.86        32.65         0.79 
TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       42.51        15.25         0.82        48.49         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       16.93        22.65         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       14.01        13.45         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       32.68        39.75        77.59       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       17.92         5.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        23.80        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             0.07              0.00 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           214.62            223.96 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           15.685            18.410 
[1] "0.1 - 214.6 (15.7)" "0.0 - 224.0 (18.4)"
[1] "hr=" "1.4"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SMARCA4 MUTATED         1        8        9         4         8          6
  SMARCA4 WILD-TYPE       3      115      124        42        59         64
                   vv
clus                STAGE IIIB STAGE IV
  SMARCA4 MUTATED            1        1
  SMARCA4 WILD-TYPE         10       24
D6V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 8               115
  STAGE IB                 9               124
  STAGE IIA                4                42
  STAGE IIB                8                59
  STAGE IIIA               6                64
  STAGE IIIB               1                10
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCA4 MUTATED    11  24   3   0
  SMARCA4 WILD-TYPE 144 237  40  18
D6V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1              11               144
  T2              24               237
  T3               3                40
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  SMARCA4 MUTATED    21  10     6
  SMARCA4 WILD-TYPE 286  79    66
D6V5, multiclass
       clus
vv      SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0                 21               286
  N1                 10                79
  N2+N3               6                66
[1] 3 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
  SMARCA4 MUTATED    32   1
  SMARCA4 WILD-TYPE 295  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     32    1
  SMARCA4 WILD-TYPE  295   22
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0              32               295
  1               1                22
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    14  24
  SMARCA4 WILD-TYPE 245 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     14   24
  SMARCA4 WILD-TYPE  245  197
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE              14               245
  MALE                24               197
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SMARCA4 MUTATED                            1
  SMARCA4 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SMARCA4 MUTATED                                   5
  SMARCA4 WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SMARCA4 MUTATED                                                   24
  SMARCA4 WILD-TYPE                                                270
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SMARCA4 MUTATED                                            1
  SMARCA4 WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SMARCA4 MUTATED                                               0
  SMARCA4 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SMARCA4 MUTATED                                0
  SMARCA4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SMARCA4 MUTATED                                    0
  SMARCA4 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SMARCA4 MUTATED                              0                             1
  SMARCA4 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SMARCA4 MUTATED                                               4
  SMARCA4 WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SMARCA4 MUTATED                              2
  SMARCA4 WILD-TYPE                            7
D6V9, multiclass
                                                    clus
vv                                                   SMARCA4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              24
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   SMARCA4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     2  36
  SMARCA4 WILD-TYPE  18 424
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      2   36
  SMARCA4 WILD-TYPE   18  424
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO                2                18
  YES              36               424
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SMARCA4 MUTATED    23   0   0   2
  SMARCA4 WILD-TYPE 287  11   4  23
D6V13, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0              23               287
  R1               0                11
  R2               0                 4
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     0
  SMARCA4 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           2    31
  SMARCA4 WILD-TYPE                        27   346
D6V14, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         31               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     3  26
  SMARCA4 WILD-TYPE   3 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      3   26
  SMARCA4 WILD-TYPE    3  323
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              26               323
[1] 2 2
[1] FALSE

Clustering(7) Variable = STK11 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  STK11 MUTATED    44  28
  STK11 WILD-TYPE 271 113
  STK11 MUTATED STK11 WILD-TYPE 
             72             384 
  STK11 MUTATED STK11 WILD-TYPE 
             28             113 
$`STK11 MUTATED`
TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4432 TCGA-05-5425 
        0.00         2.99        14.96        12.00        25.02        29.00 
TCGA-44-6144 TCGA-44-6776 TCGA-44-6779 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 
       23.77        63.72        16.44        17.59         8.55        15.98 
TCGA-44-A47F TCGA-49-4486 TCGA-49-4487 TCGA-49-4507 TCGA-50-5072 TCGA-50-5932 
       11.08        76.21        28.11         8.81         8.22        40.60 
TCGA-50-5939 TCGA-53-7813 TCGA-55-6970 TCGA-55-6983 TCGA-55-7574 TCGA-55-8092 
       15.12        13.94        15.25        60.03         3.12         5.06 
TCGA-55-8203 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 
       17.98        15.42         0.95         0.26         0.49         0.49 
TCGA-55-A492 TCGA-62-A46P TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-5774 
       19.59        19.53        54.35        39.25        40.96        87.98 
TCGA-69-7763 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-78-7148 TCGA-78-7152 
       22.68         4.31         1.25        39.09        20.58        39.52 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 
       32.09        64.90        22.29         7.07         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-86-7701 TCGA-86-7713 
       26.53        31.20         8.02        53.33        31.13        13.87 
TCGA-86-8054 TCGA-86-8280 TCGA-86-8359 TCGA-91-6849 TCGA-95-A4VP TCGA-97-8179 
       24.49        23.05        14.60         1.15        19.89        14.30 
TCGA-97-A4M3 TCGA-99-8025 TCGA-99-8032 TCGA-J2-8194 TCGA-MP-A4TD TCGA-MP-A4TE 
       17.75        34.85         1.45        23.80        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A55O TCGA-NJ-A55R 
       11.05        14.66        71.05         1.64         0.43        19.82 

$`STK11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        9.01        29.98        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 
       25.02        24.00        15.02        15.02         4.96        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        28.37        12.59        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        21.63        23.18        32.45        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B 
       29.00        23.64        12.66         3.25        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       11.54        13.64        13.45        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        14.07        32.84        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
       49.28         9.27        14.27        78.67        21.47         8.45 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        42.51        40.73         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 
        5.49         7.79         2.20        45.34        32.71        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        1.45         0.76         0.36        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
       42.38        14.60        88.64        49.25        47.80        56.71 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       67.96        72.30        13.61        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       55.43        38.37         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       29.98        26.30        15.35         1.32         5.39        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        19.27        35.93        21.90 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 
       24.99        19.50        38.50         5.88       104.19       223.96 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       34.39        20.55        19.43        19.89        16.70         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       15.85        21.47         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23        27.68         7.36        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
       27.29         2.76        21.40        18.18        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8033 
       20.84        18.67        20.68        24.56        36.76         5.59 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        5.29        41.59        31.23         2.43        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-O1-A52J 
       73.91        62.60         0.13        29.13         0.26        59.11 

  STK11 MUTATED STK11 WILD-TYPE 
           0.00            0.07 
  STK11 MUTATED STK11 WILD-TYPE 
          88.14          223.96 
  STK11 MUTATED STK11 WILD-TYPE 
          17.67           18.15 
[1] "0.0 - 88.1 (17.7)"  "0.1 - 224.0 (18.1)"
[1] "hr=" "1.3"
D7V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STK11 MUTATED         0       18       19         6        13         12
  STK11 WILD-TYPE       4      105      114        40        54         58
                 vv
clus              STAGE IIIB STAGE IV
  STK11 MUTATED            3        5
  STK11 WILD-TYPE          8       20
D7V3, multiclass
            clus
vv           STK11 MUTATED STK11 WILD-TYPE
  STAGE I                0               4
  STAGE IA              18             105
  STAGE IB              19             114
  STAGE IIA              6              40
  STAGE IIB             13              54
  STAGE IIIA            12              58
  STAGE IIIB             3               8
  STAGE IV               5              20
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK11 MUTATED    20  44   7   5
  STK11 WILD-TYPE 135 217  36  13
D7V4, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  T1            20             135
  T2            44             217
  T3             7              36
  T4             5              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"
                 vv
clus               N0  N1 N2+N3
  STK11 MUTATED    47  14    14
  STK11 WILD-TYPE 260  75    58
D7V5, multiclass
       clus
vv      STK11 MUTATED STK11 WILD-TYPE
  N0               47             260
  N1               14              75
  N2+N3            14              58
[1] 3 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
  STK11 MUTATED    55   5
  STK11 WILD-TYPE 272  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     55    5
  STK11 WILD-TYPE  272   18
   clus
vv  STK11 MUTATED STK11 WILD-TYPE
  0            55             272
  1             5              18
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus                0   1
  STK11 MUTATED    30  46
  STK11 WILD-TYPE 229 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     30   46
  STK11 WILD-TYPE  229  175
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE            30             229
  MALE              46             175
[1] 2 2
[1] FALSE
D7V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STK11 MUTATED                            4                                21
  STK11 WILD-TYPE                         14                                81
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STK11 MUTATED                                                   41
  STK11 WILD-TYPE                                                253
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STK11 MUTATED                                            0
  STK11 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STK11 MUTATED                                               3
  STK11 WILD-TYPE                                            16
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STK11 MUTATED                                0
  STK11 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STK11 MUTATED                                    0
  STK11 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STK11 MUTATED                              0                             4
  STK11 WILD-TYPE                            2                            18
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STK11 MUTATED                                               0
  STK11 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STK11 MUTATED                              3
  STK11 WILD-TYPE                            6
D7V9, multiclass
                                                    clus
vv                                                   STK11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            41
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   3
                                                    clus
vv                                                   STK11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             253
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   18
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                 cls
clus                0   1
  STK11 MUTATED     6  70
  STK11 WILD-TYPE  14 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      6   70
  STK11 WILD-TYPE   14  390
     clus
vv    STK11 MUTATED STK11 WILD-TYPE
  NO              6              14
  YES            70             390
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, continuous
                 vv
clus               R0  R1  R2  RX
  STK11 MUTATED    51   3   0   3
  STK11 WILD-TYPE 259   8   4  22
D7V13, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  R0            51             259
  R1             3               8
  R2             0               4
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK11 MUTATED                                  0     0
  STK11 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK11 MUTATED                           7    58
  STK11 WILD-TYPE                        22   319
D7V14, multiclass
                                  clus
vv                                 STK11 MUTATED STK11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    7              22
  WHITE                                       58             319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                 cls
clus                0   1
  STK11 MUTATED     0  49
  STK11 WILD-TYPE   6 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      0   49
  STK11 WILD-TYPE    6  300
                        clus
vv                       STK11 MUTATED STK11 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            49             300
[1] 2 2
[1] FALSE

Clustering(8) Variable = RB1 MUTATION ANALYSIS
D8V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    18   7
  RB1 WILD-TYPE 297 134
  RB1 MUTATED RB1 WILD-TYPE 
           25           431 
  RB1 MUTATED RB1 WILD-TYPE 
            7           134 
$`RB1 MUTATED`
TCGA-05-4397 TCGA-05-4415 TCGA-35-5375 TCGA-44-6775 TCGA-44-7660 TCGA-44-7669 
       24.03         2.99         8.68        23.18        19.46        18.87 
TCGA-55-6968 TCGA-55-8208 TCGA-55-A48Z TCGA-78-7143 TCGA-86-8056 TCGA-86-8074 
       42.51        22.16        21.40       163.10         4.57         0.79 
TCGA-86-8358 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6847 TCGA-93-A4JN 
       21.47        10.62        41.36         2.60        27.68        23.61 
TCGA-93-A4JP TCGA-95-7562 TCGA-95-7947 TCGA-97-7553 TCGA-97-8172 TCGA-J2-A4AE 
       19.00         2.86        15.68        43.79        17.92        35.47 
TCGA-L4-A4E5 
       19.00 

$`RB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       12.03         7.17        36.07        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
        0.07        32.65         0.79        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       23.51        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
       16.70        24.49         4.08        24.33        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.65        15.85        23.05        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
       17.62        13.64        26.47         1.97        10.19        13.71 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
        1.08        17.29         1.12         1.22        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        63.52        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       18.08        16.44        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  RB1 MUTATED RB1 WILD-TYPE 
         0.79          0.00 
  RB1 MUTATED RB1 WILD-TYPE 
       163.10        223.96 
  RB1 MUTATED RB1 WILD-TYPE 
        19.46         17.65 
[1] "0.8 - 163.1 (19.5)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.2"
D8V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RB1 MUTATED         1        6        8         3         1          2
  RB1 WILD-TYPE       3      117      125        43        66         68
               vv
clus            STAGE IIIB STAGE IV
  RB1 MUTATED            2        3
  RB1 WILD-TYPE          9       22
D8V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              1             3
  STAGE IA             6           117
  STAGE IB             8           125
  STAGE IIA            3            43
  STAGE IIB            1            66
  STAGE IIIA           2            68
  STAGE IIIB           2             9
  STAGE IV             3            22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  RB1 MUTATED    11  12   0   2
  RB1 WILD-TYPE 144 249  43  16
D8V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1          11           144
  T2          12           249
  T3           0            43
  T4           2            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"
               vv
clus             N0  N1 N2+N3
  RB1 MUTATED    18   4     3
  RB1 WILD-TYPE 289  85    69
D8V5, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  N0             18           289
  N1              4            85
  N2+N3           3            69
[1] 3 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
  RB1 MUTATED    15   3
  RB1 WILD-TYPE 312  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     15    3
  RB1 WILD-TYPE  312   20
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          15           312
  1           3            20
[1] 2 2
[1] FALSE
D8V7, binary
               cls
clus              0   1
  RB1 MUTATED    13  13
  RB1 WILD-TYPE 246 208
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     13   13
  RB1 WILD-TYPE  246  208
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          13           246
  MALE            13           208
[1] 2 2
[1] FALSE
D8V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RB1 MUTATED                            2                                 5
  RB1 WILD-TYPE                         16                                97
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RB1 MUTATED                                                   15
  RB1 WILD-TYPE                                                279
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RB1 MUTATED                                            0
  RB1 WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RB1 MUTATED                                               3
  RB1 WILD-TYPE                                            16
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  RB1 MUTATED                                0
  RB1 WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  RB1 MUTATED                                    0                            0
  RB1 WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  RB1 MUTATED                               1
  RB1 WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RB1 MUTATED                                               0
  RB1 WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  RB1 MUTATED                              0
  RB1 WILD-TYPE                            9
D8V9, multiclass
                                                    clus
vv                                                   RB1 MUTATED RB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   2            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            5            97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          15           279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                3            16
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
               cls
clus              0   1
  RB1 MUTATED     0  26
  RB1 WILD-TYPE  20 434
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   26
  RB1 WILD-TYPE   20  434
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            0            20
  YES          26           434
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, continuous
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    16   0   0   4
  RB1 WILD-TYPE 294  11   4  21
D8V13, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          16           294
  R1           0            11
  R2           0             4
  RX           4            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     1
  RB1 WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           2    20
  RB1 WILD-TYPE                        27   357
D8V14, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  2            27
  WHITE                                     20           357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
               cls
clus              0   1
  RB1 MUTATED     1  21
  RB1 WILD-TYPE   5 328
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   21
  RB1 WILD-TYPE    5  328
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          21           328
[1] 2 2
[1] FALSE

Clustering(9) Variable = ARID1A MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    20   9
  ARID1A WILD-TYPE 295 132
  ARID1A MUTATED ARID1A WILD-TYPE 
              29              427 
  ARID1A MUTATED ARID1A WILD-TYPE 
               9              132 
$`ARID1A MUTATED`
TCGA-05-4382 TCGA-05-4425 TCGA-05-4427 TCGA-05-5715 TCGA-38-4631 TCGA-44-6147 
       19.96        21.99        26.01         2.04        11.64        27.78 
TCGA-44-7667 TCGA-44-7670 TCGA-55-5899 TCGA-55-7725 TCGA-55-7815 TCGA-55-7914 
       36.07        29.00         2.86         1.28         1.78         6.15 
TCGA-55-8089 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-A490 TCGA-64-1681 
        3.29        15.65        22.16        15.42         1.58        38.37 
TCGA-67-3771 TCGA-78-7156 TCGA-78-7167 TCGA-86-8278 TCGA-91-6831 TCGA-97-7938 
       20.05        32.09        88.14        15.65        10.19         0.59 
TCGA-99-8025 TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MP-A4TC TCGA-MP-A4TI 
       34.85        19.00        38.63         2.43        14.10 

$`ARID1A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 
        4.96        29.00        22.03         9.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       35.28        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       10.78         9.93        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        18.87        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05        48.62         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 
       23.18         1.28         1.12         0.79         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 
       17.98         1.08         1.51         2.17         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       55.43        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       28.47        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       223.96         8.48        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        15.75        16.08        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36         1.97         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79        25.48         5.95         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
       17.75        20.84        18.67        20.68        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       16.44        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59        31.23        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.59             0.00 
  ARID1A MUTATED ARID1A WILD-TYPE 
           88.14           223.96 
  ARID1A MUTATED ARID1A WILD-TYPE 
           15.65            18.08 
[1] "0.6 - 88.1 (15.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D9V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARID1A MUTATED         1       11        5         4         3          3
  ARID1A WILD-TYPE       3      112      128        42        64         67
                  vv
clus               STAGE IIIB STAGE IV
  ARID1A MUTATED            0        3
  ARID1A WILD-TYPE         11       22
D9V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 1                3
  STAGE IA               11              112
  STAGE IB                5              128
  STAGE IIA               4               42
  STAGE IIB               3               64
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                3               22
[1] 8 2
[1] TRUE
[1] "dimension of 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    15  12   2   1
  ARID1A WILD-TYPE 140 249  41  17
D9V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1             15              140
  T2             12              249
  T3              2               41
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  ARID1A MUTATED    19   7     3
  ARID1A WILD-TYPE 288  82    69
D9V5, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  N0                19              288
  N1                 7               82
  N2+N3              3               69
[1] 3 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
  ARID1A MUTATED    18   3
  ARID1A WILD-TYPE 309  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     18    3
  ARID1A WILD-TYPE  309   20
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             18              309
  1              3               20
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    18  12
  ARID1A WILD-TYPE 241 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     18   12
  ARID1A WILD-TYPE  241  209
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             18              241
  MALE               12              209
[1] 2 2
[1] FALSE
D9V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARID1A MUTATED                            0                                 5
  ARID1A WILD-TYPE                         18                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                   23
  ARID1A WILD-TYPE                                                271
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARID1A MUTATED                                            0
  ARID1A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARID1A MUTATED                                               1
  ARID1A WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ARID1A MUTATED                                0
  ARID1A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ARID1A MUTATED                                    0
  ARID1A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARID1A MUTATED                              0                             1
  ARID1A WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARID1A MUTATED                                               0
  ARID1A WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ARID1A MUTATED                              0
  ARID1A WILD-TYPE                            9
D9V9, multiclass
                                                    clus
vv                                                   ARID1A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             23
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ARID1A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              271
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                  cls
clus                 0   1
  ARID1A MUTATED     0  30
  ARID1A WILD-TYPE  20 430
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0   30
  ARID1A WILD-TYPE   20  430
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               0               20
  YES             30              430
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, continuous
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    25   1   0   0
  ARID1A WILD-TYPE 285  10   4  25
D9V13, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             25              285
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     0
  ARID1A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           2    22
  ARID1A WILD-TYPE                        27   355
D9V14, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        22              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  21
  ARID1A WILD-TYPE   5 328
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   21
  ARID1A WILD-TYPE    5  328
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             21              328
[1] 2 2
[1] FALSE

Clustering(10) Variable = NF1 MUTATION ANALYSIS
D10V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    37  16
  NF1 WILD-TYPE 278 125
  NF1 MUTATED NF1 WILD-TYPE 
           53           403 
  NF1 MUTATED NF1 WILD-TYPE 
           16           125 
$`NF1 MUTATED`
TCGA-05-4424 TCGA-38-4629 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 TCGA-44-3918 
       30.02        28.41        11.64        46.98        13.15        34.06 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6775 TCGA-44-7667 TCGA-44-8119 TCGA-49-4488 
       28.37        23.77        23.18        36.07         3.25        28.57 
TCGA-49-6767 TCGA-50-5045 TCGA-50-5068 TCGA-50-5072 TCGA-50-5946 TCGA-50-6593 
       22.26        71.47        49.28         8.22        22.55        11.05 
TCGA-50-8457 TCGA-55-1592 TCGA-55-6971 TCGA-55-6975 TCGA-55-7724 TCGA-55-7907 
       25.61        23.05         0.82         3.88        23.18         0.53 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8205 TCGA-55-8621 TCGA-55-A4DG 
       19.82         0.16         3.29         1.08        16.93        19.99 
TCGA-62-A46S TCGA-64-1679 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
       54.35        55.43        13.61         5.42         2.30         2.93 
TCGA-73-4658 TCGA-73-4676 TCGA-78-7146 TCGA-78-7535 TCGA-78-7542 TCGA-86-8073 
       52.60         5.39         5.69        31.20        10.55        24.33 
TCGA-86-8279 TCGA-86-8669 TCGA-91-6829 TCGA-95-7043 TCGA-95-7944 TCGA-97-7547 
       15.85        30.84        41.36         1.22        12.39        64.60 
TCGA-97-7553 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MP-A4SY TCGA-NJ-A55A 
       43.79        19.00         0.20        49.35         0.26 

$`NF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       37.71        49.05        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        4.37        24.36        42.77        37.15        38.24         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       26.56        33.30        12.59        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
       14.60        19.46        12.03         7.17        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.11        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 
       29.26        17.16        11.64        20.52        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       60.16        31.04         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
       42.35         3.91        25.55        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        0.72        10.13         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94         9.21        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 
        0.79        42.51        40.73        15.25        48.49         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
        7.99         0.20         0.13         3.12         1.32         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.48        17.65         6.15        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 
       20.58        19.59         0.92        15.81        20.19         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        20.65        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 
        6.12        22.68         7.56         6.05        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24         7.04         2.01         0.10        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       29.98        26.30        15.35         4.31         1.32         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       39.09        23.51       163.10        27.16        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
      223.96         8.48        88.14        26.53         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.65        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.12         2.86        18.67        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 
        2.76        21.40        18.18        19.89        31.69        63.52 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       16.44        14.30         3.81        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64        29.13         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  NF1 MUTATED NF1 WILD-TYPE 
         0.16          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
        71.47        223.96 
  NF1 MUTATED NF1 WILD-TYPE 
        19.99         17.75 
[1] "0.2 - 71.5 (20.0)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1"  
D10V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NF1 MUTATED         1       17       18         3        11          4
  NF1 WILD-TYPE       3      106      115        43        56         66
               vv
clus            STAGE IIIB STAGE IV
  NF1 MUTATED            0        1
  NF1 WILD-TYPE         11       24
D10V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I              1             3
  STAGE IA            17           106
  STAGE IB            18           115
  STAGE IIA            3            43
  STAGE IIB           11            56
  STAGE IIIA           4            66
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NF1 MUTATED    18  30   6   1
  NF1 WILD-TYPE 137 231  37  17
D10V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1          18           137
  T2          30           231
  T3           6            37
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  NF1 MUTATED    42   8     4
  NF1 WILD-TYPE 265  81    68
D10V5, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  N0             42           265
  N1              8            81
  N2+N3           4            68
[1] 3 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
  NF1 MUTATED    33   0
  NF1 WILD-TYPE 294  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     33    0
  NF1 WILD-TYPE  294   23
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          33           294
  1           0            23
[1] 2 2
[1] FALSE
D10V7, binary
               cls
clus              0   1
  NF1 MUTATED    29  26
  NF1 WILD-TYPE 230 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     29   26
  NF1 WILD-TYPE  230  195
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          29           230
  MALE            26           195
[1] 2 2
[1] FALSE
D10V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NF1 MUTATED                            1                                10
  NF1 WILD-TYPE                         17                                92
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NF1 MUTATED                                                   39
  NF1 WILD-TYPE                                                255
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NF1 MUTATED                                            0
  NF1 WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NF1 MUTATED                                               3
  NF1 WILD-TYPE                                            16
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  NF1 MUTATED                                0
  NF1 WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  NF1 MUTATED                                    0                            0
  NF1 WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  NF1 MUTATED                               2
  NF1 WILD-TYPE                            20
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NF1 MUTATED                                               0
  NF1 WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  NF1 MUTATED                              0
  NF1 WILD-TYPE                            9
D10V9, multiclass
                                                    clus
vv                                                   NF1 MUTATED NF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           10            92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          39           255
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                3            16
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                2            20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
               cls
clus              0   1
  NF1 MUTATED     3  52
  NF1 WILD-TYPE  17 408
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      3   52
  NF1 WILD-TYPE   17  408
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            3            17
  YES          52           408
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, continuous
               vv
clus             R0  R1  R2  RX
  NF1 MUTATED    34   1   0   2
  NF1 WILD-TYPE 276  10   4  23
D10V13, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          34           276
  R1           1            10
  R2           0             4
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     0
  NF1 WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           3    50
  NF1 WILD-TYPE                        26   327
D10V14, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  3            26
  WHITE                                     50           327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
               cls
clus              0   1
  NF1 MUTATED     1  46
  NF1 WILD-TYPE   5 303
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   46
  NF1 WILD-TYPE    5  303
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          46           303
[1] 2 2
[1] FALSE

Clustering(11) Variable = BRAF MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    25  10
  BRAF WILD-TYPE 290 131
  BRAF MUTATED BRAF WILD-TYPE 
            35            421 
  BRAF MUTATED BRAF WILD-TYPE 
            10            131 
$`BRAF MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-5428 TCGA-44-2656 TCGA-44-3918 
       50.07        19.96        45.01        22.03        46.98        34.06 
TCGA-44-6774 TCGA-50-5044 TCGA-50-5930 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       21.63        20.52         9.27        18.64        29.03        22.55 
TCGA-50-6594 TCGA-53-A4EZ TCGA-55-6968 TCGA-55-6979 TCGA-55-7903 TCGA-55-8092 
       12.16         9.21        42.51         7.79        18.64         5.06 
TCGA-55-8506 TCGA-55-8511 TCGA-62-A46V TCGA-62-A472 TCGA-69-7765 TCGA-78-7153 
        0.36         0.30        72.30        29.92         5.42        24.99 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8660 TCGA-78-8662 TCGA-86-7714 
       53.33        10.75        32.68        10.55       110.50        20.55 
TCGA-91-A4BD TCGA-95-7039 TCGA-97-A4M7 TCGA-L4-A4E6 TCGA-MN-A4N1 
       19.82         1.12        20.68        14.30        27.19 

$`BRAF WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
        3.98        14.01        37.02         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
        4.96        29.00         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
       13.15        24.36        42.77        37.15        38.24         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
        9.93        27.78        23.15        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        22.26        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         8.22        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6590 
       78.67        21.47         8.45        15.12        25.12        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        11.05         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.49        17.72         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 
       54.35        67.96        13.61        39.25        40.96        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       26.53        31.20         8.02        39.35        10.55       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       39.75        77.59        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        13.87        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
        1.45         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81         0.20        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  BRAF MUTATED BRAF WILD-TYPE 
           0.3            0.0 
  BRAF MUTATED BRAF WILD-TYPE 
        110.50         223.96 
  BRAF MUTATED BRAF WILD-TYPE 
         20.55          17.62 
[1] "0.3 - 110.5 (20.6)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.2"
D11V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BRAF MUTATED         0        8       10         5         7          5
  BRAF WILD-TYPE       4      115      123        41        60         65
                vv
clus             STAGE IIIB STAGE IV
  BRAF MUTATED            1        2
  BRAF WILD-TYPE         10       23
D11V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               0              4
  STAGE IA              8            115
  STAGE IB             10            123
  STAGE IIA             5             41
  STAGE IIB             7             60
  STAGE IIIA            5             65
  STAGE IIIB            1             10
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of 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    12  19   5   2
  BRAF WILD-TYPE 143 242  38  16
D11V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1           12            143
  T2           19            242
  T3            5             38
  T4            2             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"
                vv
clus              N0  N1 N2+N3
  BRAF MUTATED    25   8     5
  BRAF WILD-TYPE 282  81    67
D11V5, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  N0              25            282
  N1               8             81
  N2+N3            5             67
[1] 3 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
  BRAF MUTATED    28   1
  BRAF WILD-TYPE 299  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     28    1
  BRAF WILD-TYPE  299   22
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           28            299
  1            1             22
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  BRAF MUTATED    16  22
  BRAF WILD-TYPE 243 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     16   22
  BRAF WILD-TYPE  243  199
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           16            243
  MALE             22            199
[1] 2 2
[1] FALSE
D11V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BRAF MUTATED                            1                                15
  BRAF WILD-TYPE                         17                                87
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BRAF MUTATED                                                   22
  BRAF WILD-TYPE                                                272
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BRAF MUTATED                                            0
  BRAF WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BRAF MUTATED                                               0
  BRAF WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  BRAF MUTATED                                0
  BRAF WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  BRAF MUTATED                                    0
  BRAF WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BRAF MUTATED                              0                             0
  BRAF WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BRAF MUTATED                                               0
  BRAF WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  BRAF MUTATED                              0
  BRAF WILD-TYPE                            9
D11V9, multiclass
                                                    clus
vv                                                   BRAF MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           22
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   BRAF WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            272
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                cls
clus               0   1
  BRAF MUTATED     3  35
  BRAF WILD-TYPE  17 425
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      3   35
  BRAF WILD-TYPE   17  425
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO             3             17
  YES           35            425
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, continuous
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    24   0   0   3
  BRAF WILD-TYPE 286  11   4  22
D11V13, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           24            286
  R1            0             11
  R2            0              4
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRAF MUTATED                                  0     0
  BRAF WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED                           4    24
  BRAF WILD-TYPE                        25   353
D11V14, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   4             25
  WHITE                                      24            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                cls
clus               0   1
  BRAF MUTATED     1  21
  BRAF WILD-TYPE   5 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1   21
  BRAF WILD-TYPE    5  328
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           21            328
[1] 2 2
[1] FALSE

Clustering(12) Variable = MGA MUTATION ANALYSIS
D12V1, survival
               sevent
clus2             0   1
  MGA MUTATED    31   9
  MGA WILD-TYPE 284 132
  MGA MUTATED MGA WILD-TYPE 
           40           416 
  MGA MUTATED MGA WILD-TYPE 
            9           132 
$`MGA MUTATED`
TCGA-05-4405 TCGA-05-4418 TCGA-05-5428 TCGA-05-5715 TCGA-35-5375 TCGA-38-4628 
       20.05         9.01        22.03         2.04         8.68        49.05 
TCGA-44-5644 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-A4SU TCGA-49-4494 
       28.37        29.00        17.59        12.66        13.45        35.54 
TCGA-49-6743 TCGA-49-6745 TCGA-50-5931 TCGA-55-6712 TCGA-55-6968 TCGA-55-7574 
       12.13        17.16        14.27         0.79        42.51         3.12 
TCGA-55-7907 TCGA-55-8208 TCGA-55-8506 TCGA-55-8511 TCGA-55-A490 TCGA-64-5779 
        0.53        22.16         0.36         0.30         1.58        28.41 
TCGA-69-7763 TCGA-69-7974 TCGA-69-A59K TCGA-71-8520 TCGA-73-4668 TCGA-78-7156 
       22.68         6.05         7.04         0.10        15.35        32.09 
TCGA-78-7220 TCGA-86-7955 TCGA-91-6829 TCGA-91-A4BD TCGA-93-A4JQ TCGA-95-7039 
       26.53        16.70        41.36        19.82        17.29         1.12 
TCGA-95-7043 TCGA-97-A4LX TCGA-L9-A443 TCGA-L9-A444 
        1.22        20.19         3.81         0.20 

$`MGA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 
       15.02         4.96        29.00         9.04         7.40         5.98 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       97.74       120.79        37.71        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
        8.81        29.46        29.75        55.89        14.63        29.26 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.22         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
       23.05        48.62         2.86         0.07        32.65        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 
        1.12         0.79         1.78         1.45        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
       55.43        38.37        87.98         2.04        42.90        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        2.01        52.60        23.38        29.98        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        38.50         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18         1.45         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 TCGA-95-7567 
        6.12        23.61         1.08        19.00         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.58        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       19.00        14.30        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  MGA MUTATED MGA WILD-TYPE 
          0.1           0.0 
  MGA MUTATED MGA WILD-TYPE 
        49.05        223.96 
  MGA MUTATED MGA WILD-TYPE 
       14.810        18.655 
[1] "0.1 - 49.0 (14.8)"  "0.0 - 224.0 (18.7)"
[1] "hr=" "1.2"
D12V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MGA MUTATED         0        7       12         6         5          8
  MGA WILD-TYPE       4      116      121        40        62         62
               vv
clus            STAGE IIIB STAGE IV
  MGA MUTATED            0        2
  MGA WILD-TYPE         11       23
D12V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              0             4
  STAGE IA             7           116
  STAGE IB            12           121
  STAGE IIA            6            40
  STAGE IIB            5            62
  STAGE IIIA           8            62
  STAGE IIIB           0            11
  STAGE IV             2            23
[1] 8 2
[1] TRUE
[1] "dimension of 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    12  22   5   1
  MGA WILD-TYPE 143 239  38  17
D12V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1          12           143
  T2          22           239
  T3           5            38
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  MGA MUTATED    24   8     8
  MGA WILD-TYPE 283  81    64
D12V5, multiclass
       clus
vv      MGA MUTATED MGA WILD-TYPE
  N0             24           283
  N1              8            81
  N2+N3           8            64
[1] 3 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
  MGA MUTATED    22   2
  MGA WILD-TYPE 305  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     22    2
  MGA WILD-TYPE  305   21
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          22           305
  1           2            21
[1] 2 2
[1] FALSE
D12V7, binary
               cls
clus              0   1
  MGA MUTATED    22  18
  MGA WILD-TYPE 237 203
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     22   18
  MGA WILD-TYPE  237  203
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          22           237
  MALE            18           203
[1] 2 2
[1] FALSE
D12V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MGA MUTATED                            2                                13
  MGA WILD-TYPE                         16                                89
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                   22
  MGA WILD-TYPE                                                272
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MGA MUTATED                                            0
  MGA WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MGA MUTATED                                               1
  MGA WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MGA MUTATED                                1
  MGA WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MGA MUTATED                                    1                            0
  MGA WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MGA MUTATED                               0
  MGA WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MGA MUTATED                                               0
  MGA WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MGA MUTATED                              0
  MGA WILD-TYPE                            9
D12V9, multiclass
                                                    clus
vv                                                   MGA MUTATED MGA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   2            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           13            89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          22           272
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           1             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
               cls
clus              0   1
  MGA MUTATED     4  36
  MGA WILD-TYPE  16 424
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      4   36
  MGA WILD-TYPE   16  424
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO            4            16
  YES          36           424
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, continuous
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    22   1   0   3
  MGA WILD-TYPE 288  10   4  22
D12V13, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          22           288
  R1           1            10
  R2           0             4
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGA MUTATED                                  1     1
  MGA WILD-TYPE                                0     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MGA MUTATED                           2    32
  MGA WILD-TYPE                        27   345
D12V14, multiclass
                                  clus
vv                                 MGA MUTATED MGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  2            27
  WHITE                                     32           345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
               cls
clus              0   1
  MGA MUTATED     1  30
  MGA WILD-TYPE   5 319
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      1   30
  MGA WILD-TYPE    5  319
                        clus
vv                       MGA MUTATED MGA WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          30           319
[1] 2 2
[1] FALSE

Clustering(13) Variable = CHRND MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  CHRND MUTATED    15   2
  CHRND WILD-TYPE 300 139
  CHRND MUTATED CHRND WILD-TYPE 
             17             439 
  CHRND MUTATED CHRND WILD-TYPE 
              2             139 
$`CHRND MUTATED`
TCGA-05-4418 TCGA-05-4420 TCGA-05-4432 TCGA-38-4632 TCGA-44-3918 TCGA-44-5644 
        9.01        29.98        25.02        44.61        34.06        28.37 
TCGA-44-7662 TCGA-44-A479 TCGA-50-5049 TCGA-50-8459 TCGA-55-7907 TCGA-55-8302 
        7.17        15.98        70.55         7.59         0.53         0.76 
TCGA-55-A492 TCGA-62-8399 TCGA-64-5778 TCGA-86-8358 TCGA-95-7947 
       19.59        88.64        42.90        21.47        15.68 

$`CHRND WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       20.05         2.99        14.96        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        6.25        26.56        33.30        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 
        1.22         2.86        18.67        12.39        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CHRND MUTATED CHRND WILD-TYPE 
           0.53            0.00 
  CHRND MUTATED CHRND WILD-TYPE 
          88.64          223.96 
  CHRND MUTATED CHRND WILD-TYPE 
          21.47           17.92 
[1] "0.5 - 88.6 (21.5)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "3.4"
D13V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CHRND MUTATED         0        4        8         1         2          2
  CHRND WILD-TYPE       4      119      125        45        65         68
                 vv
clus              STAGE IIIB STAGE IV
  CHRND MUTATED            0        1
  CHRND WILD-TYPE         11       24
D13V3, multiclass
            clus
vv           CHRND MUTATED CHRND WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               8             125
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHRND MUTATED     3  13   2   0
  CHRND WILD-TYPE 152 248  41  18
D13V4, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  T1             3             152
  T2            13             248
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  CHRND MUTATED    13   3     2
  CHRND WILD-TYPE 294  86    70
D13V5, multiclass
       clus
vv      CHRND MUTATED CHRND WILD-TYPE
  N0               13             294
  N1                3              86
  N2+N3             2              70
[1] 3 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
  CHRND MUTATED    11   1
  CHRND WILD-TYPE 316  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED     11    1
  CHRND WILD-TYPE  316   22
   clus
vv  CHRND MUTATED CHRND WILD-TYPE
  0            11             316
  1             1              22
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  CHRND MUTATED     5  13
  CHRND WILD-TYPE 254 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      5   13
  CHRND WILD-TYPE  254  208
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  FEMALE             5             254
  MALE              13             208
[1] 2 2
[1] FALSE
D13V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHRND MUTATED                            0                                 4
  CHRND WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHRND MUTATED                                                   11
  CHRND WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CHRND MUTATED                                            0
  CHRND WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CHRND MUTATED                                               1
  CHRND WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CHRND MUTATED                                0
  CHRND WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CHRND MUTATED                                    0
  CHRND WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CHRND MUTATED                              0                             1
  CHRND WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CHRND MUTATED                                               0
  CHRND WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CHRND MUTATED                              1
  CHRND WILD-TYPE                            8
D13V9, multiclass
                                                    clus
vv                                                   CHRND MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   CHRND WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                 cls
clus                0   1
  CHRND MUTATED     1  17
  CHRND WILD-TYPE  19 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      1   17
  CHRND WILD-TYPE   19  443
     clus
vv    CHRND MUTATED CHRND WILD-TYPE
  NO              1              19
  YES            17             443
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, continuous
                 vv
clus               R0  R1  R2  RX
  CHRND MUTATED    14   0   0   0
  CHRND WILD-TYPE 296  11   4  25
D13V13, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  R0            14             296
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRND MUTATED                                  0     0
  CHRND WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRND MUTATED                           2    12
  CHRND WILD-TYPE                        27   365
D13V14, multiclass
                                  clus
vv                                 CHRND MUTATED CHRND WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                 cls
clus                0   1
  CHRND MUTATED     0  13
  CHRND WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      0   13
  CHRND WILD-TYPE    6  336
                        clus
vv                       CHRND MUTATED CHRND WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(14) Variable = MET MUTATION ANALYSIS
D14V1, survival
               sevent
clus2             0   1
  MET MUTATED    13   6
  MET WILD-TYPE 302 135
  MET MUTATED MET WILD-TYPE 
           19           437 
  MET MUTATED MET WILD-TYPE 
            6           135 
$`MET MUTATED`
TCGA-05-4403 TCGA-44-2657 TCGA-44-7671 TCGA-44-A47G TCGA-49-6745 TCGA-49-6761 
       19.00        13.15        17.59        11.54        17.16        11.64 
TCGA-50-5930 TCGA-50-5933 TCGA-50-6597 TCGA-55-6712 TCGA-55-6982 TCGA-55-8511 
        9.27        78.67        41.69         0.79        32.71         0.30 
TCGA-64-5781 TCGA-78-7143 TCGA-86-8358 TCGA-91-6847 TCGA-93-7348 TCGA-97-8176 
       51.25       163.10        21.47        27.68         4.18        15.39 
TCGA-J2-A4AE 
       35.47 

$`MET WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 
        0.00         9.96        24.03        47.05         8.02        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        46.98        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.08        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       14.63        12.13        29.26        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       23.05        48.62         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       38.37        87.98         2.04        42.90        28.41        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1.25        39.09        23.51        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
       14.27         1.18         1.45        19.82         9.76         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92         5.39        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  MET MUTATED MET WILD-TYPE 
          0.3           0.0 
  MET MUTATED MET WILD-TYPE 
       163.10        223.96 
  MET MUTATED MET WILD-TYPE 
        17.59         18.08 
[1] "0.3 - 163.1 (17.6)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D14V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MET MUTATED         0        3       11         1         1          4
  MET WILD-TYPE       4      120      122        45        66         66
               vv
clus            STAGE IIIB STAGE IV
  MET MUTATED            1        0
  MET WILD-TYPE         10       25
D14V3, multiclass
            clus
vv           MET MUTATED MET WILD-TYPE
  STAGE I              0             4
  STAGE IA             3           120
  STAGE IB            11           122
  STAGE IIA            1            45
  STAGE IIB            1            66
  STAGE IIIA           4            66
  STAGE IIIB           1            10
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MET MUTATED     4  15   1   1
  MET WILD-TYPE 151 246  42  17
D14V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1           4           151
  T2          15           246
  T3           1            42
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  MET MUTATED    13   3     4
  MET WILD-TYPE 294  86    68
D14V5, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  N0             13           294
  N1              3            86
  N2+N3           4            68
[1] 3 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
  MET MUTATED    15   0
  MET WILD-TYPE 312  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     15    0
  MET WILD-TYPE  312   23
   clus
vv  MET MUTATED MET WILD-TYPE
  0          15           312
  1           0            23
[1] 2 2
[1] FALSE
D14V7, binary
               cls
clus              0   1
  MET MUTATED    12   9
  MET WILD-TYPE 247 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     12    9
  MET WILD-TYPE  247  212
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE          12           247
  MALE             9           212
[1] 2 2
[1] FALSE
D14V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MET MUTATED                            1                                 4
  MET WILD-TYPE                         17                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MET MUTATED                                                   15
  MET WILD-TYPE                                                279
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MET MUTATED                                            0
  MET WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MET MUTATED                                               1
  MET WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MET MUTATED                                0
  MET WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MET MUTATED                                    0                            0
  MET WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MET MUTATED                               0
  MET WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MET MUTATED                                               0
  MET WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MET MUTATED                              0
  MET WILD-TYPE                            9
D14V9, multiclass
                                                    clus
vv                                                   MET MUTATED MET WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          15           279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
               cls
clus              0   1
  MET MUTATED     2  19
  MET WILD-TYPE  18 441
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      2   19
  MET WILD-TYPE   18  441
     clus
vv    MET MUTATED MET WILD-TYPE
  NO            2            18
  YES          19           441
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, continuous
               vv
clus             R0  R1  R2  RX
  MET MUTATED    14   0   0   0
  MET WILD-TYPE 296  11   4  25
D14V13, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  R0          14           296
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           1    17
  MET WILD-TYPE                        28   360
D14V14, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     17           360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
               cls
clus              0   1
  MET MUTATED     0  14
  MET WILD-TYPE   6 335
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      0   14
  MET WILD-TYPE    6  335
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          14           335
[1] 2 2
[1] FALSE

Clustering(15) Variable = CDKN2A MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    13   3
  CDKN2A WILD-TYPE 302 138
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              440 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               3              138 
$`CDKN2A MUTATED`
TCGA-05-4426 TCGA-05-4433 TCGA-38-4625 TCGA-38-6178 TCGA-44-5645 TCGA-44-7662 
       26.01        24.00        97.74        14.73        12.59         7.17 
TCGA-49-4505 TCGA-50-6595 TCGA-53-A4EZ TCGA-55-8205 TCGA-55-A492 TCGA-67-3771 
       14.07         6.21         9.21         1.08        19.59        20.05 
TCGA-78-7148 TCGA-86-8585 TCGA-93-8067 TCGA-97-8547 
       20.58         1.15         6.12        21.60 

$`CDKN2A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 
       30.02        21.99        26.01        25.02        25.02        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        44.61        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       34.06         6.25        26.56        33.30        28.37        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       12.03        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        46.72        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        20.58         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        21.47        14.60        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        9.76         4.18        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        14.30        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1.08             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           97.74           223.96 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            14.4             18.1 
[1] "1.1 - 97.7 (14.4)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D15V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CDKN2A MUTATED         0        3        6         1         3          3
  CDKN2A WILD-TYPE       4      120      127        45        64         67
                  vv
clus               STAGE IIIB STAGE IV
  CDKN2A MUTATED            0        0
  CDKN2A WILD-TYPE         11       25
D15V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                6              127
  STAGE IIA               1               45
  STAGE IIB               3               64
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     3  13   0   0
  CDKN2A WILD-TYPE 152 248  43  18
D15V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              3              152
  T2             13              248
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  CDKN2A MUTATED     9   3     3
  CDKN2A WILD-TYPE 298  86    69
D15V5, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  N0                 9              298
  N1                 3               86
  N2+N3              3               69
[1] 3 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
  CDKN2A MUTATED     9   0
  CDKN2A WILD-TYPE 318  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      9    0
  CDKN2A WILD-TYPE  318   23
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0              9              318
  1              0               23
[1] 2 2
[1] FALSE
D15V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     9   7
  CDKN2A WILD-TYPE 250 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      9    7
  CDKN2A WILD-TYPE  250  214
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              9              250
  MALE                7              214
[1] 2 2
[1] FALSE
D15V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CDKN2A MUTATED                            1                                 4
  CDKN2A WILD-TYPE                         17                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                   10
  CDKN2A WILD-TYPE                                                284
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CDKN2A MUTATED                                            0
  CDKN2A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CDKN2A MUTATED                                               0
  CDKN2A WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CDKN2A MUTATED                                0
  CDKN2A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CDKN2A MUTATED                                    0
  CDKN2A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CDKN2A MUTATED                              0                             0
  CDKN2A WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CDKN2A MUTATED                                               1
  CDKN2A WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CDKN2A MUTATED                              0
  CDKN2A WILD-TYPE                            9
D15V9, multiclass
                                                    clus
vv                                                   CDKN2A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CDKN2A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     0  16
  CDKN2A WILD-TYPE  20 444
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   16
  CDKN2A WILD-TYPE   20  444
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               0               20
  YES             16              444
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, continuous
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED     9   1   0   2
  CDKN2A WILD-TYPE 301  10   4  23
D15V13, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0              9              301
  R1              1               10
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKN2A MUTATED                                  0     1
  CDKN2A WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED                           2    10
  CDKN2A WILD-TYPE                        27   367
D15V14, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     1  11
  CDKN2A WILD-TYPE   5 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   11
  CDKN2A WILD-TYPE    5  338
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(16) Variable = U2AF1 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  U2AF1 MUTATED     9   3
  U2AF1 WILD-TYPE 306 138
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             12             444 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              3             138 
$`U2AF1 MUTATED`
TCGA-49-4505 TCGA-49-6743 TCGA-49-6744 TCGA-50-5941 TCGA-50-8460 TCGA-55-1595 
       14.07        12.13        29.26        18.64        27.25        48.62 
TCGA-55-7727 TCGA-55-7903 TCGA-78-7145 TCGA-78-8655 TCGA-86-8585 TCGA-MP-A4T4 
        1.12        18.64        27.16        77.59         1.15        86.04 

$`U2AF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        46.72        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
       29.46        29.75        55.89        14.63        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47         8.45        15.12        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 
       34.29        30.54        13.94         9.21        23.05         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       39.09        23.51       163.10         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  U2AF1 MUTATED U2AF1 WILD-TYPE 
           1.12            0.00 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          86.04          223.96 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
         22.900          17.835 
[1] "1.1 - 86.0 (22.9)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.7"
D16V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  U2AF1 MUTATED         0        4        1         1         2          3
  U2AF1 WILD-TYPE       4      119      132        45        65         67
                 vv
clus              STAGE IIIB STAGE IV
  U2AF1 MUTATED            0        1
  U2AF1 WILD-TYPE         11       24
D16V3, multiclass
            clus
vv           U2AF1 MUTATED U2AF1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               1             132
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  U2AF1 MUTATED     6   5   0   1
  U2AF1 WILD-TYPE 149 256  43  17
D16V4, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  T1             6             149
  T2             5             256
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  U2AF1 MUTATED     5   4     3
  U2AF1 WILD-TYPE 302  85    69
D16V5, multiclass
       clus
vv      U2AF1 MUTATED U2AF1 WILD-TYPE
  N0                5             302
  N1                4              85
  N2+N3             3              69
[1] 3 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
  U2AF1 MUTATED     7   1
  U2AF1 WILD-TYPE 320  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      7    1
  U2AF1 WILD-TYPE  320   22
   clus
vv  U2AF1 MUTATED U2AF1 WILD-TYPE
  0             7             320
  1             1              22
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  U2AF1 MUTATED     8   4
  U2AF1 WILD-TYPE 251 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      8    4
  U2AF1 WILD-TYPE  251  217
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  FEMALE             8             251
  MALE               4             217
[1] 2 2
[1] FALSE
D16V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  U2AF1 MUTATED                            0                                 2
  U2AF1 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  U2AF1 MUTATED                                                    6
  U2AF1 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  U2AF1 MUTATED                                            0
  U2AF1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  U2AF1 MUTATED                                               0
  U2AF1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  U2AF1 MUTATED                                2
  U2AF1 WILD-TYPE                              0
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  U2AF1 MUTATED                                    0
  U2AF1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  U2AF1 MUTATED                              0                             1
  U2AF1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  U2AF1 MUTATED                                               1
  U2AF1 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  U2AF1 MUTATED                              0
  U2AF1 WILD-TYPE                            9
D16V9, multiclass
                                                    clus
vv                                                   U2AF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   U2AF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                 cls
clus                0   1
  U2AF1 MUTATED     0  12
  U2AF1 WILD-TYPE  20 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      0   12
  U2AF1 WILD-TYPE   20  448
     clus
vv    U2AF1 MUTATED U2AF1 WILD-TYPE
  NO              0              20
  YES            12             448
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, continuous
                 vv
clus               R0  R1  R2  RX
  U2AF1 MUTATED     8   1   0   0
  U2AF1 WILD-TYPE 302  10   4  25
D16V13, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  R0             8             302
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  U2AF1 MUTATED                                  0     1
  U2AF1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  U2AF1 MUTATED                           0    10
  U2AF1 WILD-TYPE                        29   367
D16V14, multiclass
                                  clus
vv                                 U2AF1 MUTATED U2AF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                 cls
clus                0   1
  U2AF1 MUTATED     0   6
  U2AF1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      0    6
  U2AF1 WILD-TYPE    6  343
                        clus
vv                       U2AF1 MUTATED U2AF1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(17) Variable = SETD2 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    15  10
  SETD2 WILD-TYPE 300 131
  SETD2 MUTATED SETD2 WILD-TYPE 
             25             431 
  SETD2 MUTATED SETD2 WILD-TYPE 
             10             131 
$`SETD2 MUTATED`
TCGA-05-4425 TCGA-05-4427 TCGA-38-4631 TCGA-49-4487 TCGA-49-6744 TCGA-50-5941 
       21.99        26.01        11.64        28.11        29.26        18.64 
TCGA-50-5942 TCGA-53-7624 TCGA-55-6986 TCGA-55-A4DF TCGA-62-A46P TCGA-64-5775 
       29.03        34.29       107.21        20.19        19.53         2.04 
TCGA-67-6216 TCGA-69-7760 TCGA-73-4658 TCGA-73-4666 TCGA-73-4676 TCGA-78-7150 
        4.64         6.64        52.60        26.30         5.39        21.90 
TCGA-86-7714 TCGA-86-8278 TCGA-91-6848 TCGA-97-7941 TCGA-97-A4M6 TCGA-97-A4M7 
       20.55        15.65         7.36         0.72        18.67        20.68 
TCGA-MP-A4SY 
       49.35 

$`SETD2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       30.02        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       14.63        12.13        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        8.45        15.12        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       60.03        24.99        40.54        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        47.80        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       55.43        38.37        87.98        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 
       28.47        20.05        18.84        14.04         5.72        13.87 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
        7.04         2.01         0.10        23.38        29.98        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        4.31         1.32         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
       27.16         5.69        19.27        20.58        35.93        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       13.87        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        4.57        24.33         0.79        15.75        16.08        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23        27.68         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 
       19.76        20.52        17.75        20.84        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
       27.19        38.63         2.76        86.14        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.72            0.00 
  SETD2 MUTATED SETD2 WILD-TYPE 
         107.21          223.96 
  SETD2 MUTATED SETD2 WILD-TYPE 
          20.55           17.65 
[1] "0.7 - 107.2 (20.6)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.3"
D17V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SETD2 MUTATED         0        7        6         2         6          6
  SETD2 WILD-TYPE       4      116      127        44        61         64
                 vv
clus              STAGE IIIB STAGE IV
  SETD2 MUTATED            0        3
  SETD2 WILD-TYPE         11       22
D17V3, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             116
  STAGE IB               6             127
  STAGE IIA              2              44
  STAGE IIB              6              61
  STAGE IIIA             6              64
  STAGE IIIB             0              11
  STAGE IV               3              22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SETD2 MUTATED     9  18   2   1
  SETD2 WILD-TYPE 146 243  41  17
D17V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             9             146
  T2            18             243
  T3             2              41
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  SETD2 MUTATED    18   7     5
  SETD2 WILD-TYPE 289  82    67
D17V5, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  N0               18             289
  N1                7              82
  N2+N3             5              67
[1] 3 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
  SETD2 MUTATED    22   3
  SETD2 WILD-TYPE 305  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     22    3
  SETD2 WILD-TYPE  305   20
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            22             305
  1             3              20
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    20  10
  SETD2 WILD-TYPE 239 211
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     20   10
  SETD2 WILD-TYPE  239  211
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            20             239
  MALE              10             211
[1] 2 2
[1] FALSE
D17V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SETD2 MUTATED                            2                                 7
  SETD2 WILD-TYPE                         16                                95
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SETD2 MUTATED                                                   19
  SETD2 WILD-TYPE                                                275
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SETD2 MUTATED                                            0
  SETD2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SETD2 MUTATED                                               1
  SETD2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SETD2 MUTATED                                0
  SETD2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SETD2 MUTATED                                    0
  SETD2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SETD2 MUTATED                              0                             1
  SETD2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SETD2 MUTATED                                               0
  SETD2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SETD2 MUTATED                              0
  SETD2 WILD-TYPE                            9
D17V9, multiclass
                                                    clus
vv                                                   SETD2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SETD2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             275
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                 cls
clus                0   1
  SETD2 MUTATED     3  27
  SETD2 WILD-TYPE  17 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      3   27
  SETD2 WILD-TYPE   17  433
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO              3              17
  YES            27             433
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, continuous
                 vv
clus               R0  R1  R2  RX
  SETD2 MUTATED    23   1   1   0
  SETD2 WILD-TYPE 287  10   3  25
D17V13, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            23             287
  R1             1              10
  R2             1               3
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           1    23
  SETD2 WILD-TYPE                        28   354
D17V14, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       23             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  19
  SETD2 WILD-TYPE   5 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   19
  SETD2 WILD-TYPE    5  330
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            19             330
[1] 2 2
[1] FALSE

Clustering(18) Variable = DNMT3A MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED    13   5
  DNMT3A WILD-TYPE 302 136
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              18              438 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               5              136 
$`DNMT3A MUTATED`
TCGA-44-7662 TCGA-50-5931 TCGA-50-6595 TCGA-55-6987 TCGA-55-8089 TCGA-55-8207 
        7.17        14.27         6.21        70.26         3.29         2.17 
TCGA-55-A490 TCGA-64-5774 TCGA-64-5778 TCGA-86-8073 TCGA-86-8672 TCGA-91-6830 
        1.58        87.98        42.90        24.33         0.62         1.97 
TCGA-91-8499 TCGA-97-7547 TCGA-97-8176 TCGA-97-8179 TCGA-MP-A4TA TCGA-NJ-A4YQ 
        1.18        64.60        15.39        14.30        31.23        29.13 

$`DNMT3A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       14.60         1.15        13.91        30.84        27.58        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
        7.36         1.15        16.18        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.18        19.89        31.69        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       18.12        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
            0.62             0.00 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           87.98           223.96 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
          14.285           18.150 
[1] "0.6 - 88.0 (14.3)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D18V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DNMT3A MUTATED         0        6        7         2         1          2
  DNMT3A WILD-TYPE       4      117      126        44        66         68
                  vv
clus               STAGE IIIB STAGE IV
  DNMT3A MUTATED            0        0
  DNMT3A WILD-TYPE         11       25
D18V3, multiclass
            clus
vv           DNMT3A MUTATED DNMT3A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                6              117
  STAGE IB                7              126
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNMT3A MUTATED     7   9   2   0
  DNMT3A WILD-TYPE 148 252  41  18
D18V4, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  T1              7              148
  T2              9              252
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  DNMT3A MUTATED    15   2     1
  DNMT3A WILD-TYPE 292  87    71
D18V5, multiclass
       clus
vv      DNMT3A MUTATED DNMT3A WILD-TYPE
  N0                15              292
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  DNMT3A MUTATED    12   0
  DNMT3A WILD-TYPE 315  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     12    0
  DNMT3A WILD-TYPE  315   23
   clus
vv  DNMT3A MUTATED DNMT3A WILD-TYPE
  0             12              315
  1              0               23
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     7  11
  DNMT3A WILD-TYPE 252 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      7   11
  DNMT3A WILD-TYPE  252  210
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              7              252
  MALE               11              210
[1] 2 2
[1] FALSE
D18V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DNMT3A MUTATED                            3                                 0
  DNMT3A WILD-TYPE                         15                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DNMT3A MUTATED                                                   12
  DNMT3A WILD-TYPE                                                282
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DNMT3A MUTATED                                            0
  DNMT3A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DNMT3A MUTATED                                               2
  DNMT3A WILD-TYPE                                            17
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  DNMT3A MUTATED                                0
  DNMT3A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  DNMT3A MUTATED                                    0
  DNMT3A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DNMT3A MUTATED                              0                             1
  DNMT3A WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DNMT3A MUTATED                                               0
  DNMT3A WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  DNMT3A MUTATED                              0
  DNMT3A WILD-TYPE                            9
D18V9, multiclass
                                                    clus
vv                                                   DNMT3A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   DNMT3A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    17
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     0  18
  DNMT3A WILD-TYPE  20 442
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0   18
  DNMT3A WILD-TYPE   20  442
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               0               20
  YES             18              442
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, continuous
                  vv
clus                R0  R1  R2  RX
  DNMT3A MUTATED    10   0   0   1
  DNMT3A WILD-TYPE 300  11   4  24
D18V13, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  R0             10              300
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNMT3A MUTATED                                  0     0
  DNMT3A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED                           0    18
  DNMT3A WILD-TYPE                        29   359
D18V14, multiclass
                                  clus
vv                                 DNMT3A MUTATED DNMT3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        18              359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     0  18
  DNMT3A WILD-TYPE   6 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0   18
  DNMT3A WILD-TYPE    6  331
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             18              331
[1] 2 2
[1] FALSE

Clustering(19) Variable = ERBB2 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED     8   3
  ERBB2 WILD-TYPE 307 138
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             445 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              3             138 
$`ERBB2 MUTATED`
TCGA-05-4384 TCGA-05-4434 TCGA-05-5715 TCGA-38-4629 TCGA-44-2656 TCGA-44-3396 
       14.01        15.02         2.04        28.41        46.98        37.15 
TCGA-44-3919 TCGA-44-A47B TCGA-86-6562 TCGA-86-A456 TCGA-95-7567 
        6.25         9.44        12.36        13.32        18.67 

$`ERBB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-4122 
       15.02         4.96        29.00        22.03         9.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
       13.15        24.36        42.77        38.24        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.98        15.32        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        14.96        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.22         2.86        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           2.04            0.00 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          46.98          223.96 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          14.01           18.12 
[1] "2.0 - 47.0 (14.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D19V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ERBB2 MUTATED         0        2        3         1         2          2
  ERBB2 WILD-TYPE       4      121      130        45        65         68
                 vv
clus              STAGE IIIB STAGE IV
  ERBB2 MUTATED            0        1
  ERBB2 WILD-TYPE         11       24
D19V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               3             130
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   7   1   1
  ERBB2 WILD-TYPE 153 254  42  17
D19V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             2             153
  T2             7             254
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  ERBB2 MUTATED     6   3     2
  ERBB2 WILD-TYPE 301  86    70
D19V5, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  N0                6             301
  N1                3              86
  N2+N3             2              70
[1] 3 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
  ERBB2 MUTATED    10   1
  ERBB2 WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     10    1
  ERBB2 WILD-TYPE  317   22
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            10             317
  1             1              22
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED     5   6
  ERBB2 WILD-TYPE 254 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      5    6
  ERBB2 WILD-TYPE  254  215
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             5             254
  MALE               6             215
[1] 2 2
[1] FALSE
D19V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ERBB2 MUTATED                            0                                 4
  ERBB2 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                    6
  ERBB2 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ERBB2 MUTATED                                            0
  ERBB2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ERBB2 MUTATED                                               0
  ERBB2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ERBB2 MUTATED                                0
  ERBB2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ERBB2 MUTATED                                    0
  ERBB2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ERBB2 MUTATED                              0                             1
  ERBB2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ERBB2 MUTATED                                               0
  ERBB2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ERBB2 MUTATED                              0
  ERBB2 WILD-TYPE                            9
D19V9, multiclass
                                                    clus
vv                                                   ERBB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ERBB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                 cls
clus                0   1
  ERBB2 MUTATED     0  11
  ERBB2 WILD-TYPE  20 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0   11
  ERBB2 WILD-TYPE   20  449
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              0              20
  YES            11             449
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, continuous
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED     7   0   1   1
  ERBB2 WILD-TYPE 303  11   3  24
D19V13, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             1               3
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB2 MUTATED                                  0     1
  ERBB2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED                           0     7
  ERBB2 WILD-TYPE                        29   370
D19V14, multiclass
                                  clus
vv                                 ERBB2 MUTATED ERBB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                 cls
clus                0   1
  ERBB2 MUTATED     0   8
  ERBB2 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0    8
  ERBB2 WILD-TYPE    6  341
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(20) Variable = ATM MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  ATM MUTATED    27  12
  ATM WILD-TYPE 288 129
  ATM MUTATED ATM WILD-TYPE 
           39           417 
  ATM MUTATED ATM WILD-TYPE 
           12           129 
$`ATM MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4417 TCGA-49-4486 TCGA-49-4507 TCGA-49-4510 
       19.96        37.02        14.96        76.21         8.81        29.46 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1595 TCGA-55-6642 TCGA-55-6971 TCGA-55-7815 
       34.29        13.94        48.62        32.65         0.82         1.78 
TCGA-55-8508 TCGA-62-8398 TCGA-62-A46Y TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        0.49        14.60        13.61        38.37        87.98         2.04 
TCGA-67-6215 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8255 
        5.72         7.56         2.30         2.93        14.01         4.24 
TCGA-73-4659 TCGA-78-7156 TCGA-78-7159 TCGA-78-7539 TCGA-86-8054 TCGA-86-A4JF 
       23.38        32.09        64.90        10.75        24.49        17.62 
TCGA-93-A4JN TCGA-95-7567 TCGA-95-A4VP TCGA-97-8176 TCGA-97-A4M3 TCGA-L9-A443 
       23.61        18.67        19.89        15.39        17.75         3.81 
TCGA-MN-A4N4 TCGA-MP-A4TI TCGA-NJ-A4YP 
       38.63        14.10         1.64 

$`ATM WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       14.07        32.84        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        25.61         7.59        27.25        30.54 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
        9.21        23.05         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        72.30        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       56.81        20.65        55.43        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6216 TCGA-67-6217 
       28.47        20.05        18.84        14.04         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
        6.64         6.12        22.68        13.61         5.42         6.05 
TCGA-69-7980 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       12.56        13.45         7.04         2.01         0.10        52.60 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50         5.88        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       16.70         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO 
        1.45        19.82         9.76         4.18         6.12         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
       19.00        17.29         1.12         1.22         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       19.76        20.52        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
       18.08        35.47        16.44        19.00        14.30         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        2.43        10.09        29.46        11.05        14.66        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ATM MUTATED ATM WILD-TYPE 
         0.49          0.00 
  ATM MUTATED ATM WILD-TYPE 
        87.98        223.96 
  ATM MUTATED ATM WILD-TYPE 
        15.39         18.18 
[1] "0.5 - 88.0 (15.4)"  "0.0 - 224.0 (18.2)"
[1] "hr=" "1.1"
D20V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ATM MUTATED         0        9       11         4         6          7
  ATM WILD-TYPE       4      114      122        42        61         63
               vv
clus            STAGE IIIB STAGE IV
  ATM MUTATED            1        4
  ATM WILD-TYPE         10       21
D20V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I              0             4
  STAGE IA             9           114
  STAGE IB            11           122
  STAGE IIA            4            42
  STAGE IIB            6            61
  STAGE IIIA           7            63
  STAGE IIIB           1            10
  STAGE IV             4            21
[1] 8 2
[1] TRUE
[1] "dimension of 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    10  26   3   3
  ATM WILD-TYPE 145 235  40  15
D20V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1          10           145
  T2          26           235
  T3           3            40
  T4           3            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"
               vv
clus             N0  N1 N2+N3
  ATM MUTATED    25  11     5
  ATM WILD-TYPE 282  78    67
D20V5, multiclass
       clus
vv      ATM MUTATED ATM WILD-TYPE
  N0             25           282
  N1             11            78
  N2+N3           5            67
[1] 3 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
  ATM MUTATED    30   4
  ATM WILD-TYPE 297  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     30    4
  ATM WILD-TYPE  297   19
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          30           297
  1           4            19
[1] 2 2
[1] FALSE
D20V7, binary
               cls
clus              0   1
  ATM MUTATED    22  20
  ATM WILD-TYPE 237 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     22   20
  ATM WILD-TYPE  237  201
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          22           237
  MALE            20           201
[1] 2 2
[1] FALSE
D20V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ATM MUTATED                            5                                13
  ATM WILD-TYPE                         13                                89
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ATM MUTATED                                                   19
  ATM WILD-TYPE                                                275
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ATM MUTATED                                            0
  ATM WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ATM MUTATED                                               1
  ATM WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  ATM MUTATED                                1
  ATM WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  ATM MUTATED                                    0                            0
  ATM WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  ATM MUTATED                               1
  ATM WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ATM MUTATED                                               1
  ATM WILD-TYPE                                             4
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  ATM MUTATED                              1
  ATM WILD-TYPE                            8
D20V9, multiclass
                                                    clus
vv                                                   ATM MUTATED ATM WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   5            13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           13            89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          19           275
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                1             4
  MUCINOUS (COLLOID) CARCINOMA                                 1             8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
               cls
clus              0   1
  ATM MUTATED     1  41
  ATM WILD-TYPE  19 419
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1   41
  ATM WILD-TYPE   19  419
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO            1            19
  YES          41           419
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, continuous
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    29   0   0   2
  ATM WILD-TYPE 281  11   4  23
D20V13, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          29           281
  R1           0            11
  R2           0             4
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     1
  ATM WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED                           3    31
  ATM WILD-TYPE                        26   346
D20V14, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  3            26
  WHITE                                     31           346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, binary
               cls
clus              0   1
  ATM MUTATED     2  27
  ATM WILD-TYPE   4 322
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      2   27
  ATM WILD-TYPE    4  322
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               2             4
  NOT HISPANIC OR LATINO          27           322
[1] 2 2
[1] FALSE

Clustering(21) Variable = COL5A2 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2                0   1
  COL5A2 MUTATED    32  14
  COL5A2 WILD-TYPE 283 127
  COL5A2 MUTATED COL5A2 WILD-TYPE 
              46              410 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
              14              127 
$`COL5A2 MUTATED`
TCGA-05-4382 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4405 TCGA-05-4420 
       19.96         0.00         9.96        24.03        20.05        29.98 
TCGA-05-5423 TCGA-38-4631 TCGA-44-2656 TCGA-44-5644 TCGA-44-6145 TCGA-44-7660 
        4.96        11.64        46.98        28.37        10.78        19.46 
TCGA-44-7669 TCGA-44-7670 TCGA-44-A47G TCGA-49-6761 TCGA-50-5049 TCGA-50-6590 
       18.87        29.00        11.54        11.64        70.55        42.35 
TCGA-50-6593 TCGA-50-6594 TCGA-55-6968 TCGA-55-7570 TCGA-55-7815 TCGA-55-7994 
       11.05        12.16        42.51         0.20         1.78        19.82 
TCGA-55-8089 TCGA-55-A48X TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 TCGA-62-A46O 
        3.29        22.65        20.19        19.99        88.64        47.80 
TCGA-64-5774 TCGA-64-5779 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-73-4666 
       87.98        28.41         6.05         2.93        12.56        26.30 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7536 TCGA-86-8073 TCGA-86-A4JF TCGA-97-7554 
       19.50        38.50         8.02        24.33        17.62        25.48 
TCGA-97-8179 TCGA-99-8032 TCGA-L4-A4E5 TCGA-MN-A4N4 
       14.30         1.45        19.00        38.63 

$`COL5A2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
       50.07         3.98        14.01        45.01        37.02        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 
        8.02        19.00         2.99        14.96         9.01        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       38.24        34.06         6.25        26.56        33.30        12.59 
TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       23.77         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
       63.72        32.45        61.28        16.44        14.60        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        36.07        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.08        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6767 
       55.89        14.63        12.13        29.26        17.16        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
        3.91        25.55         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1.15         7.99         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 
        1.28         1.28         1.12         0.79         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       15.81         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       38.37         2.04        42.90        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
        6.12        22.68        13.61         5.42         7.56         2.30 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       24.99        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       17.92         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81         0.20        27.19         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  COL5A2 MUTATED COL5A2 WILD-TYPE 
            0.00             0.07 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
           88.64           223.96 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
          19.660           17.685 
[1] "0.0 - 88.6 (19.7)"  "0.1 - 224.0 (17.7)"
[1] "hr=" "1"  
D21V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL5A2 MUTATED         2       10       15         3         4         10
  COL5A2 WILD-TYPE       2      113      118        43        63         60
                  vv
clus               STAGE IIIB STAGE IV
  COL5A2 MUTATED            2        2
  COL5A2 WILD-TYPE          9       23
D21V3, multiclass
            clus
vv           COL5A2 MUTATED COL5A2 WILD-TYPE
  STAGE I                 2                2
  STAGE IA               10              113
  STAGE IB               15              118
  STAGE IIA               3               43
  STAGE IIB               4               63
  STAGE IIIA             10               60
  STAGE IIIB              2                9
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL5A2 MUTATED    18  24   4   2
  COL5A2 WILD-TYPE 137 237  39  16
D21V4, multiclass
    clus
vv   COL5A2 MUTATED COL5A2 WILD-TYPE
  T1             18              137
  T2             24              237
  T3              4               39
  T4              2               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"
                  vv
clus                N0  N1 N2+N3
  COL5A2 MUTATED    31   6    11
  COL5A2 WILD-TYPE 276  83    61
D21V5, multiclass
       clus
vv      COL5A2 MUTATED COL5A2 WILD-TYPE
  N0                31              276
  N1                 6               83
  N2+N3             11               61
[1] 3 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
  COL5A2 MUTATED    35   2
  COL5A2 WILD-TYPE 292  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED     35    2
  COL5A2 WILD-TYPE  292   21
   clus
vv  COL5A2 MUTATED COL5A2 WILD-TYPE
  0             35              292
  1              2               21
[1] 2 2
[1] FALSE
D21V7, binary
                  cls
clus                 0   1
  COL5A2 MUTATED    19  29
  COL5A2 WILD-TYPE 240 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED     19   29
  COL5A2 WILD-TYPE  240  192
        clus
vv       COL5A2 MUTATED COL5A2 WILD-TYPE
  FEMALE             19              240
  MALE               29              192
[1] 2 2
[1] FALSE
D21V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL5A2 MUTATED                            3                                 9
  COL5A2 WILD-TYPE                         15                                93
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL5A2 MUTATED                                                   33
  COL5A2 WILD-TYPE                                                261
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL5A2 MUTATED                                            0
  COL5A2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL5A2 MUTATED                                               1
  COL5A2 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  COL5A2 MUTATED                                0
  COL5A2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  COL5A2 MUTATED                                    0
  COL5A2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL5A2 MUTATED                              0                             2
  COL5A2 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL5A2 MUTATED                                               0
  COL5A2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  COL5A2 MUTATED                              0
  COL5A2 WILD-TYPE                            9
D21V9, multiclass
                                                    clus
vv                                                   COL5A2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             33
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   COL5A2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              261
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                  cls
clus                 0   1
  COL5A2 MUTATED     5  43
  COL5A2 WILD-TYPE  15 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED      5   43
  COL5A2 WILD-TYPE   15  417
     clus
vv    COL5A2 MUTATED COL5A2 WILD-TYPE
  NO               5               15
  YES             43              417
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, continuous
                  vv
clus                R0  R1  R2  RX
  COL5A2 MUTATED    34   0   0   0
  COL5A2 WILD-TYPE 276  11   4  25
D21V13, multiclass
    clus
vv   COL5A2 MUTATED COL5A2 WILD-TYPE
  R0             34              276
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL5A2 MUTATED                                  0     0
  COL5A2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL5A2 MUTATED                           3    35
  COL5A2 WILD-TYPE                        26   342
D21V14, multiclass
                                  clus
vv                                 COL5A2 MUTATED COL5A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                        35              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
                  cls
clus                 0   1
  COL5A2 MUTATED     1  34
  COL5A2 WILD-TYPE   5 315
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED      1   34
  COL5A2 WILD-TYPE    5  315
                        clus
vv                       COL5A2 MUTATED COL5A2 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             34              315
[1] 2 2
[1] FALSE

Clustering(22) Variable = NFE2L2 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     6   7
  NFE2L2 WILD-TYPE 309 134
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              443 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               7              134 
$`NFE2L2 MUTATED`
TCGA-05-4422 TCGA-50-5930 TCGA-55-6975 TCGA-55-6982 TCGA-55-A48Y TCGA-62-8395 
       12.00         9.27         3.88        32.71        20.71        39.98 
TCGA-62-A471 TCGA-73-4658 TCGA-78-8660 TCGA-93-8067 TCGA-97-7941 TCGA-97-8174 
       40.96        52.60        10.55         6.12         0.72         5.39 
TCGA-J2-A4AD 
       18.08 

$`NFE2L2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 
       20.05         2.99        14.96         9.01        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
        5.49         7.79         2.20        45.34        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        16.93        22.65        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
        4.57        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       39.25        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 
        4.24         7.04         2.01         0.10        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
      214.62        39.75        77.59       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        4.18        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
       36.76         1.45         5.59        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.72             0.00 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           52.60           223.96 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           12.00            18.12 
[1] "0.7 - 52.6 (12.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.1"
D22V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NFE2L2 MUTATED         0        2        3         2         5          1
  NFE2L2 WILD-TYPE       4      121      130        44        62         69
                  vv
clus               STAGE IIIB STAGE IV
  NFE2L2 MUTATED            0        0
  NFE2L2 WILD-TYPE         11       25
D22V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                3              130
  STAGE IIA               2               44
  STAGE IIB               5               62
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFE2L2 MUTATED     2  10   1   0
  NFE2L2 WILD-TYPE 153 251  42  18
D22V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              2              153
  T2             10              251
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  NFE2L2 MUTATED     8   4     1
  NFE2L2 WILD-TYPE 299  85    71
D22V5, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0                 8              299
  N1                 4               85
  N2+N3              1               71
[1] 3 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
  NFE2L2 MUTATED    10   0
  NFE2L2 WILD-TYPE 317  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     10    0
  NFE2L2 WILD-TYPE  317   23
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0             10              317
  1              0               23
[1] 2 2
[1] FALSE
D22V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     5   8
  NFE2L2 WILD-TYPE 254 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      5    8
  NFE2L2 WILD-TYPE  254  213
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              5              254
  MALE                8              213
[1] 2 2
[1] FALSE
D22V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NFE2L2 MUTATED                            1                                 4
  NFE2L2 WILD-TYPE                         17                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NFE2L2 MUTATED                                                    7
  NFE2L2 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NFE2L2 MUTATED                                            0
  NFE2L2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NFE2L2 MUTATED                                               0
  NFE2L2 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  NFE2L2 MUTATED                                0
  NFE2L2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  NFE2L2 MUTATED                                    0
  NFE2L2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NFE2L2 MUTATED                              0                             1
  NFE2L2 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NFE2L2 MUTATED                                               0
  NFE2L2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  NFE2L2 MUTATED                              0
  NFE2L2 WILD-TYPE                            9
D22V9, multiclass
                                                    clus
vv                                                   NFE2L2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   NFE2L2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     1  12
  NFE2L2 WILD-TYPE  19 448
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      1   12
  NFE2L2 WILD-TYPE   19  448
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               1               19
  YES             12              448
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, continuous
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED     7   0   0   2
  NFE2L2 WILD-TYPE 303  11   4  23
D22V13, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0              7              303
  R1              0               11
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     1
  NFE2L2 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           0    10
  NFE2L2 WILD-TYPE                        29   367
D22V14, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  10
  NFE2L2 WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   10
  NFE2L2 WILD-TYPE    6  339
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(23) Variable = PPP3CA MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2                0   1
  PPP3CA MUTATED    11   1
  PPP3CA WILD-TYPE 304 140
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              444 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               1              140 
$`PPP3CA MUTATED`
TCGA-05-4422 TCGA-44-5643 TCGA-55-8085 TCGA-55-8514 TCGA-73-4676 TCGA-78-8662 
       12.00        33.30        29.72         6.64         5.39       110.50 
TCGA-86-8585 TCGA-91-8496 TCGA-J2-8194 TCGA-MN-A4N5 TCGA-MP-A5C7 TCGA-NJ-A4YP 
        1.15        16.60        23.80         2.76        73.91         1.64 

$`PPP3CA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 
       20.05         2.99        14.96         9.01        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15        19.82         0.16        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.30         0.10         4.80        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        4.31         1.32         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       15.65        15.85        23.05        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.18        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.30         3.81         0.20        27.19        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        14.10        19.13        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13        29.13         0.26         0.43        19.82        59.11 

  PPP3CA MUTATED PPP3CA WILD-TYPE 
            1.15             0.00 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
          110.50           223.96 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
            14.3             18.1 
[1] "1.1 - 110.5 (14.3)" "0.0 - 224.0 (18.1)"
[1] "hr=" "4.7"
D23V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PPP3CA MUTATED         0        2        7         1         1          1
  PPP3CA WILD-TYPE       4      121      126        45        66         69
                  vv
clus               STAGE IIIB STAGE IV
  PPP3CA MUTATED            0        0
  PPP3CA WILD-TYPE         11       25
D23V3, multiclass
            clus
vv           PPP3CA MUTATED PPP3CA WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                7              126
  STAGE IIA               1               45
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   9   1   0
  PPP3CA WILD-TYPE 153 252  42  18
D23V4, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  T1              2              153
  T2              9              252
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  PPP3CA MUTATED     9   1     1
  PPP3CA WILD-TYPE 298  88    71
D23V5, multiclass
       clus
vv      PPP3CA MUTATED PPP3CA WILD-TYPE
  N0                 9              298
  N1                 1               88
  N2+N3              1               71
[1] 3 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
  PPP3CA MUTATED     9   0
  PPP3CA WILD-TYPE 318  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      9    0
  PPP3CA WILD-TYPE  318   23
   clus
vv  PPP3CA MUTATED PPP3CA WILD-TYPE
  0              9              318
  1              0               23
[1] 2 2
[1] FALSE
D23V7, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     5   7
  PPP3CA WILD-TYPE 254 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      5    7
  PPP3CA WILD-TYPE  254  214
        clus
vv       PPP3CA MUTATED PPP3CA WILD-TYPE
  FEMALE              5              254
  MALE                7              214
[1] 2 2
[1] FALSE
D23V8, continuous
[1] "Remove cluster labels:" "PPP3CA MUTATED"        
clus
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-73-4668       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PPP3CA MUTATED                            0                                 2
  PPP3CA WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PPP3CA MUTATED                                                    6
  PPP3CA WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PPP3CA MUTATED                                            0
  PPP3CA WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PPP3CA MUTATED                                               1
  PPP3CA WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  PPP3CA MUTATED                                0
  PPP3CA WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  PPP3CA MUTATED                                    0
  PPP3CA WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PPP3CA MUTATED                              0                             2
  PPP3CA WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PPP3CA MUTATED                                               1
  PPP3CA WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  PPP3CA MUTATED                              0
  PPP3CA WILD-TYPE                            9
D23V9, multiclass
                                                    clus
vv                                                   PPP3CA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   PPP3CA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     2  10
  PPP3CA WILD-TYPE  18 450
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      2   10
  PPP3CA WILD-TYPE   18  450
     clus
vv    PPP3CA MUTATED PPP3CA WILD-TYPE
  NO               2               18
  YES             10              450
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, continuous
                  vv
clus                R0  R1  R2  RX
  PPP3CA MUTATED     8   0   0   0
  PPP3CA WILD-TYPE 302  11   4  25
D23V13, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  R0              8              302
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP3CA MUTATED                                  0     0
  PPP3CA WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PPP3CA MUTATED                           2     8
  PPP3CA WILD-TYPE                        27   369
D23V14, multiclass
                                  clus
vv                                 PPP3CA MUTATED PPP3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                         8              369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     0  10
  PPP3CA WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      0   10
  PPP3CA WILD-TYPE    6  339
                        clus
vv                       PPP3CA MUTATED PPP3CA WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(24) Variable = FCRLA MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  FCRLA MUTATED    10   4
  FCRLA WILD-TYPE 305 137
  FCRLA MUTATED FCRLA WILD-TYPE 
             14             442 
  FCRLA MUTATED FCRLA WILD-TYPE 
              4             137 
$`FCRLA MUTATED`
TCGA-44-2656 TCGA-44-A479 TCGA-50-5933 TCGA-50-6593 TCGA-50-6594 TCGA-55-6970 
       46.98        15.98        78.67        11.05        12.16        15.25 
TCGA-55-7576 TCGA-55-8089 TCGA-69-7973 TCGA-91-8499 TCGA-91-A4BC TCGA-95-A4VN 
        1.32         3.29         7.56         1.18         1.45        18.18 
TCGA-99-7458 TCGA-MN-A4N5 
       24.56         2.76 

$`FCRLA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 
       25.12        22.55        42.35         3.91        25.55         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         3.12        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         5.42         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       16.60        14.27        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        18.67        20.68        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  FCRLA MUTATED FCRLA WILD-TYPE 
           1.18            0.00 
  FCRLA MUTATED FCRLA WILD-TYPE 
          78.67          223.96 
  FCRLA MUTATED FCRLA WILD-TYPE 
         11.605          18.640 
[1] "1.2 - 78.7 (11.6)"  "0.0 - 224.0 (18.6)"
[1] "hr=" "1.2"
D24V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FCRLA MUTATED         0        3        5         2         0          4
  FCRLA WILD-TYPE       4      120      128        44        67         66
                 vv
clus              STAGE IIIB STAGE IV
  FCRLA MUTATED            1        0
  FCRLA WILD-TYPE         10       25
D24V3, multiclass
            clus
vv           FCRLA MUTATED FCRLA WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               5             128
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             4              66
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FCRLA MUTATED     4   8   1   2
  FCRLA WILD-TYPE 151 253  42  16
D24V4, multiclass
    clus
vv   FCRLA MUTATED FCRLA WILD-TYPE
  T1             4             151
  T2             8             253
  T3             1              42
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  FCRLA MUTATED    10   1     4
  FCRLA WILD-TYPE 297  88    68
D24V5, multiclass
       clus
vv      FCRLA MUTATED FCRLA WILD-TYPE
  N0               10             297
  N1                1              88
  N2+N3             4              68
[1] 3 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
  FCRLA MUTATED    11   0
  FCRLA WILD-TYPE 316  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED     11    0
  FCRLA WILD-TYPE  316   23
   clus
vv  FCRLA MUTATED FCRLA WILD-TYPE
  0            11             316
  1             0              23
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  FCRLA MUTATED     8   7
  FCRLA WILD-TYPE 251 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      8    7
  FCRLA WILD-TYPE  251  214
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  FEMALE             8             251
  MALE               7             214
[1] 2 2
[1] FALSE
D24V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FCRLA MUTATED                            0                                 3
  FCRLA WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FCRLA MUTATED                                                    9
  FCRLA WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FCRLA MUTATED                                            0
  FCRLA WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FCRLA MUTATED                                               1
  FCRLA WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FCRLA MUTATED                                0
  FCRLA WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FCRLA MUTATED                                    0
  FCRLA WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FCRLA MUTATED                              0                             1
  FCRLA WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FCRLA MUTATED                                               1
  FCRLA WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FCRLA MUTATED                              0
  FCRLA WILD-TYPE                            9
D24V9, multiclass
                                                    clus
vv                                                   FCRLA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FCRLA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                 cls
clus                0   1
  FCRLA MUTATED     1  14
  FCRLA WILD-TYPE  19 446
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      1   14
  FCRLA WILD-TYPE   19  446
     clus
vv    FCRLA MUTATED FCRLA WILD-TYPE
  NO              1              19
  YES            14             446
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, continuous
                 vv
clus               R0  R1  R2  RX
  FCRLA MUTATED     7   1   0   1
  FCRLA WILD-TYPE 303  10   4  24
D24V13, multiclass
    clus
vv   FCRLA MUTATED FCRLA WILD-TYPE
  R0             7             303
  R1             1              10
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FCRLA MUTATED                                  0     0
  FCRLA WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FCRLA MUTATED                           3    11
  FCRLA WILD-TYPE                        26   366
D24V14, multiclass
                                  clus
vv                                 FCRLA MUTATED FCRLA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              26
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                 cls
clus                0   1
  FCRLA MUTATED     0  13
  FCRLA WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      0   13
  FCRLA WILD-TYPE    6  336
                        clus
vv                       FCRLA MUTATED FCRLA WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(25) Variable = ARID2 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    17   7
  ARID2 WILD-TYPE 298 134
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             432 
  ARID2 MUTATED ARID2 WILD-TYPE 
              7             134 
$`ARID2 MUTATED`
TCGA-05-4396 TCGA-05-4397 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 TCGA-44-8120 
        9.96        24.03        11.64        46.98        13.15         8.55 
TCGA-50-5931 TCGA-50-6592 TCGA-55-7726 TCGA-55-7994 TCGA-55-8089 TCGA-55-8511 
       14.27        25.55         1.28        19.82         3.29         0.30 
TCGA-62-A46P TCGA-67-6217 TCGA-69-7974 TCGA-69-7978 TCGA-73-4658 TCGA-73-4675 
       19.53        13.87         6.05         2.30        52.60         1.32 
TCGA-78-7633 TCGA-86-6851 TCGA-91-6848 TCGA-91-6849 TCGA-93-8067 TCGA-MN-A4N4 
       32.68         5.88         7.36         1.15         6.12        38.63 

$`ARID2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        0.00        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        4.37        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       20.05        18.84        14.04         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 
        6.12        22.68        13.61         5.42         7.56         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       10.55       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8496 
        2.60        13.71        12.23        27.68        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ARID2 MUTATED ARID2 WILD-TYPE 
            0.3             0.0 
  ARID2 MUTATED ARID2 WILD-TYPE 
          52.60          223.96 
  ARID2 MUTATED ARID2 WILD-TYPE 
          10.80           18.64 
[1] "0.3 - 52.6 (10.8)"  "0.0 - 224.0 (18.6)"
[1] "hr=" "1.5"
D25V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARID2 MUTATED         0        4       10         2         3          4
  ARID2 WILD-TYPE       4      119      123        44        64         66
                 vv
clus              STAGE IIIB STAGE IV
  ARID2 MUTATED            1        0
  ARID2 WILD-TYPE         10       25
D25V3, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB              10             123
  STAGE IIA              2              44
  STAGE IIB              3              64
  STAGE IIIA             4              66
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of 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     4  17   2   1
  ARID2 WILD-TYPE 151 244  41  17
D25V4, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  T1             4             151
  T2            17             244
  T3             2              41
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  ARID2 MUTATED    14   6     3
  ARID2 WILD-TYPE 293  83    69
D25V5, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  N0               14             293
  N1                6              83
  N2+N3             3              69
[1] 3 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
  ARID2 MUTATED    16   0
  ARID2 WILD-TYPE 311  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     16    0
  ARID2 WILD-TYPE  311   23
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            16             311
  1             0              23
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  ARID2 MUTATED    11  13
  ARID2 WILD-TYPE 248 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     11   13
  ARID2 WILD-TYPE  248  208
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            11             248
  MALE              13             208
[1] 2 2
[1] FALSE
D25V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARID2 MUTATED                            0                                 7
  ARID2 WILD-TYPE                         18                                95
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID2 MUTATED                                                   17
  ARID2 WILD-TYPE                                                277
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARID2 MUTATED                                            0
  ARID2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARID2 MUTATED                                               0
  ARID2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ARID2 MUTATED                                0
  ARID2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ARID2 MUTATED                                    0
  ARID2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARID2 MUTATED                              0                             0
  ARID2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARID2 MUTATED                                               0
  ARID2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ARID2 MUTATED                              0
  ARID2 WILD-TYPE                            9
D25V9, multiclass
                                                    clus
vv                                                   ARID2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ARID2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                 cls
clus                0   1
  ARID2 MUTATED     1  23
  ARID2 WILD-TYPE  19 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   23
  ARID2 WILD-TYPE   19  437
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO              1              19
  YES            23             437
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, continuous
                 vv
clus               R0  R1  R2  RX
  ARID2 MUTATED    14   0   0   2
  ARID2 WILD-TYPE 296  11   4  23
D25V13, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  R0            14             296
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID2 MUTATED                                  0     1
  ARID2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED                           2    19
  ARID2 WILD-TYPE                        27   358
D25V14, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       19             358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, binary
                 cls
clus                0   1
  ARID2 MUTATED     0  21
  ARID2 WILD-TYPE   6 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      0   21
  ARID2 WILD-TYPE    6  328
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            21             328
[1] 2 2
[1] FALSE

Clustering(26) Variable = SLAMF9 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  SLAMF9 MUTATED     9   3
  SLAMF9 WILD-TYPE 306 138
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              444 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
               3              138 
$`SLAMF9 MUTATED`
TCGA-44-3918 TCGA-50-5930 TCGA-53-7624 TCGA-55-1592 TCGA-55-8506 TCGA-55-8507 
       34.06         9.27        34.29        23.05         0.36         0.26 
TCGA-78-7539 TCGA-86-8075 TCGA-86-8358 TCGA-95-7567 TCGA-97-7554 TCGA-L9-A443 
       10.75        15.75        21.47        18.67        25.48         3.81 

$`SLAMF9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        38.24         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        30.54        13.94         9.21 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20         8.02        53.33        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57        24.33         0.79        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         1.22         2.86        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
       18.08        35.47        16.44        19.00        14.30         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
            0.26             0.00 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
           34.29           223.96 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
           17.21            18.03 
[1] "0.3 - 34.3 (17.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.3"
D26V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLAMF9 MUTATED         0        4        2         1         2          2
  SLAMF9 WILD-TYPE       4      119      131        45        65         68
                  vv
clus               STAGE IIIB STAGE IV
  SLAMF9 MUTATED            0        1
  SLAMF9 WILD-TYPE         11       24
D26V3, multiclass
            clus
vv           SLAMF9 MUTATED SLAMF9 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                2              131
  STAGE IIA               1               45
  STAGE IIB               2               65
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLAMF9 MUTATED     3   8   1   0
  SLAMF9 WILD-TYPE 152 253  42  18
D26V4, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  T1              3              152
  T2              8              253
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  SLAMF9 MUTATED     9   1     2
  SLAMF9 WILD-TYPE 298  88    70
D26V5, multiclass
       clus
vv      SLAMF9 MUTATED SLAMF9 WILD-TYPE
  N0                 9              298
  N1                 1               88
  N2+N3              2               70
[1] 3 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
  SLAMF9 MUTATED     8   1
  SLAMF9 WILD-TYPE 319  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      8    1
  SLAMF9 WILD-TYPE  319   22
   clus
vv  SLAMF9 MUTATED SLAMF9 WILD-TYPE
  0              8              319
  1              1               22
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     7   5
  SLAMF9 WILD-TYPE 252 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      7    5
  SLAMF9 WILD-TYPE  252  216
        clus
vv       SLAMF9 MUTATED SLAMF9 WILD-TYPE
  FEMALE              7              252
  MALE                5              216
[1] 2 2
[1] FALSE
D26V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLAMF9 MUTATED                            0                                 3
  SLAMF9 WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLAMF9 MUTATED                                                    8
  SLAMF9 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLAMF9 MUTATED                                            0
  SLAMF9 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLAMF9 MUTATED                                               0
  SLAMF9 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SLAMF9 MUTATED                                0
  SLAMF9 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SLAMF9 MUTATED                                    0
  SLAMF9 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLAMF9 MUTATED                              0                             1
  SLAMF9 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLAMF9 MUTATED                                               0
  SLAMF9 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SLAMF9 MUTATED                              0
  SLAMF9 WILD-TYPE                            9
D26V9, multiclass
                                                    clus
vv                                                   SLAMF9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SLAMF9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     1  11
  SLAMF9 WILD-TYPE  19 449
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      1   11
  SLAMF9 WILD-TYPE   19  449
     clus
vv    SLAMF9 MUTATED SLAMF9 WILD-TYPE
  NO               1               19
  YES             11              449
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, continuous
                  vv
clus                R0  R1  R2  RX
  SLAMF9 MUTATED    10   0   0   0
  SLAMF9 WILD-TYPE 300  11   4  25
D26V13, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  R0             10              300
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLAMF9 MUTATED                                  0     0
  SLAMF9 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLAMF9 MUTATED                           0    12
  SLAMF9 WILD-TYPE                        29   365
D26V14, multiclass
                                  clus
vv                                 SLAMF9 MUTATED SLAMF9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        12              365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     1  10
  SLAMF9 WILD-TYPE   5 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      1   10
  SLAMF9 WILD-TYPE    5  339
                        clus
vv                       SLAMF9 MUTATED SLAMF9 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(27) Variable = SLC4A3 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  SLC4A3 MUTATED    12   6
  SLC4A3 WILD-TYPE 303 135
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              438 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               6              135 
$`SLC4A3 MUTATED`
TCGA-44-2656 TCGA-44-5644 TCGA-49-4488 TCGA-50-5066 TCGA-50-5946 TCGA-55-8205 
       46.98        28.37        28.57        31.04        22.55         1.08 
TCGA-62-A46R TCGA-64-5778 TCGA-64-5781 TCGA-69-7978 TCGA-69-7980 TCGA-78-7156 
       56.71        42.90        51.25         2.30        12.56        32.09 
TCGA-78-7536 TCGA-91-6840 TCGA-95-7043 TCGA-95-7567 TCGA-MP-A4SY TCGA-MP-A4TA 
        8.02        12.23         1.22        18.67        49.35        31.23 

$`SLC4A3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.11        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65        17.98         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       87.98         2.04        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        38.50         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        13.71        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       17.29         1.12         2.86        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       58.45        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
            1.08             0.00 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           56.71           223.96 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
          28.470           17.735 
[1] "1.1 - 56.7 (28.5)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "1.1"
D27V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC4A3 MUTATED         1        5        6         0         4          1
  SLC4A3 WILD-TYPE       3      118      127        46        63         69
                  vv
clus               STAGE IIIB STAGE IV
  SLC4A3 MUTATED            0        1
  SLC4A3 WILD-TYPE         11       24
D27V3, multiclass
            clus
vv           SLC4A3 MUTATED SLC4A3 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                5              118
  STAGE IB                6              127
  STAGE IIA               0               46
  STAGE IIB               4               63
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC4A3 MUTATED     6  11   0   1
  SLC4A3 WILD-TYPE 149 250  43  17
D27V4, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  T1              6              149
  T2             11              250
  T3              0               43
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  SLC4A3 MUTATED    13   4     1
  SLC4A3 WILD-TYPE 294  85    71
D27V5, multiclass
       clus
vv      SLC4A3 MUTATED SLC4A3 WILD-TYPE
  N0                13              294
  N1                 4               85
  N2+N3              1               71
[1] 3 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
  SLC4A3 MUTATED    12   1
  SLC4A3 WILD-TYPE 315  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED     12    1
  SLC4A3 WILD-TYPE  315   22
   clus
vv  SLC4A3 MUTATED SLC4A3 WILD-TYPE
  0             12              315
  1              1               22
[1] 2 2
[1] FALSE
D27V7, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED     9   9
  SLC4A3 WILD-TYPE 250 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      9    9
  SLC4A3 WILD-TYPE  250  212
        clus
vv       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  FEMALE              9              250
  MALE                9              212
[1] 2 2
[1] FALSE
D27V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC4A3 MUTATED                            0                                 8
  SLC4A3 WILD-TYPE                         18                                94
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC4A3 MUTATED                                                    9
  SLC4A3 WILD-TYPE                                                285
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC4A3 MUTATED                                            0
  SLC4A3 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC4A3 MUTATED                                               1
  SLC4A3 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SLC4A3 MUTATED                                0
  SLC4A3 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC4A3 MUTATED                                    0
  SLC4A3 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC4A3 MUTATED                              0                             0
  SLC4A3 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC4A3 MUTATED                                               0
  SLC4A3 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SLC4A3 MUTATED                              0
  SLC4A3 WILD-TYPE                            9
D27V9, multiclass
                                                    clus
vv                                                   SLC4A3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SLC4A3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED     1  17
  SLC4A3 WILD-TYPE  19 443
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      1   17
  SLC4A3 WILD-TYPE   19  443
     clus
vv    SLC4A3 MUTATED SLC4A3 WILD-TYPE
  NO               1               19
  YES             17              443
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, continuous
                  vv
clus                R0  R1  R2  RX
  SLC4A3 MUTATED    11   0   0   0
  SLC4A3 WILD-TYPE 299  11   4  25
D27V13, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  R0             11              299
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC4A3 MUTATED                                  0     0
  SLC4A3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC4A3 MUTATED                           1    17
  SLC4A3 WILD-TYPE                        28   360
D27V14, multiclass
                                  clus
vv                                 SLC4A3 MUTATED SLC4A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        17              360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED     0  15
  SLC4A3 WILD-TYPE   6 334
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      0   15
  SLC4A3 WILD-TYPE    6  334
                        clus
vv                       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             15              334
[1] 2 2
[1] FALSE

Clustering(28) Variable = SP100 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  SP100 MUTATED    15   1
  SP100 WILD-TYPE 300 140
  SP100 MUTATED SP100 WILD-TYPE 
             16             440 
  SP100 MUTATED SP100 WILD-TYPE 
              1             140 
$`SP100 MUTATED`
TCGA-38-4625 TCGA-44-7670 TCGA-44-A4SS TCGA-49-6743 TCGA-49-6767 TCGA-55-6642 
       97.74        29.00        13.64        12.13        22.26        32.65 
TCGA-55-7994 TCGA-55-8208 TCGA-55-8614 TCGA-78-7633 TCGA-86-8278 TCGA-86-A4JF 
       19.82        22.16        17.62        32.68        15.65        17.62 
TCGA-97-7554 TCGA-99-8033 TCGA-MP-A4TF TCGA-NJ-A4YP 
       25.48         5.59        11.05         1.64 

$`SP100 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       55.89        14.63        29.26        17.16        11.64        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 
       17.72         0.30         0.10         4.80         6.64         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        10.75        39.35        10.55       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       15.75        16.08        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       10.09        29.46        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         0.13        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SP100 MUTATED SP100 WILD-TYPE 
           1.64            0.00 
  SP100 MUTATED SP100 WILD-TYPE 
          97.74          223.96 
  SP100 MUTATED SP100 WILD-TYPE 
          18.72           18.03 
[1] "1.6 - 97.7 (18.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "4.9"
D28V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SP100 MUTATED         0        3        4         2         4          2
  SP100 WILD-TYPE       4      120      129        44        63         68
                 vv
clus              STAGE IIIB STAGE IV
  SP100 MUTATED            0        1
  SP100 WILD-TYPE         11       24
D28V3, multiclass
            clus
vv           SP100 MUTATED SP100 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               4             129
  STAGE IIA              2              44
  STAGE IIB              4              63
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of 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     4   8   3   0
  SP100 WILD-TYPE 151 253  40  18
D28V4, multiclass
    clus
vv   SP100 MUTATED SP100 WILD-TYPE
  T1             4             151
  T2             8             253
  T3             3              40
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  SP100 MUTATED    11   2     2
  SP100 WILD-TYPE 296  87    70
D28V5, multiclass
       clus
vv      SP100 MUTATED SP100 WILD-TYPE
  N0               11             296
  N1                2              87
  N2+N3             2              70
[1] 3 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
  SP100 MUTATED    10   1
  SP100 WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED     10    1
  SP100 WILD-TYPE  317   22
   clus
vv  SP100 MUTATED SP100 WILD-TYPE
  0            10             317
  1             1              22
[1] 2 2
[1] FALSE
D28V7, binary
                 cls
clus                0   1
  SP100 MUTATED     9   7
  SP100 WILD-TYPE 250 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED      9    7
  SP100 WILD-TYPE  250  214
        clus
vv       SP100 MUTATED SP100 WILD-TYPE
  FEMALE             9             250
  MALE               7             214
[1] 2 2
[1] FALSE
D28V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SP100 MUTATED                            0                                 1
  SP100 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SP100 MUTATED                                                   12
  SP100 WILD-TYPE                                                282
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SP100 MUTATED                                            0
  SP100 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SP100 MUTATED                                               0
  SP100 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SP100 MUTATED                                1
  SP100 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SP100 MUTATED                                    0
  SP100 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SP100 MUTATED                              0                             2
  SP100 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SP100 MUTATED                                               0
  SP100 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SP100 MUTATED                              0
  SP100 WILD-TYPE                            9
D28V9, multiclass
                                                    clus
vv                                                   SP100 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SP100 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                 cls
clus                0   1
  SP100 MUTATED     0  16
  SP100 WILD-TYPE  20 444
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED      0   16
  SP100 WILD-TYPE   20  444
     clus
vv    SP100 MUTATED SP100 WILD-TYPE
  NO              0              20
  YES            16             444
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, continuous
                 vv
clus               R0  R1  R2  RX
  SP100 MUTATED    12   0   0   0
  SP100 WILD-TYPE 298  11   4  25
D28V13, multiclass
    clus
vv   SP100 MUTATED SP100 WILD-TYPE
  R0            12             298
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SP100 MUTATED                                  0     0
  SP100 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SP100 MUTATED                           0    16
  SP100 WILD-TYPE                        29   361
D28V14, multiclass
                                  clus
vv                                 SP100 MUTATED SP100 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       16             361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                 cls
clus                0   1
  SP100 MUTATED     1  11
  SP100 WILD-TYPE   5 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED      1   11
  SP100 WILD-TYPE    5  338
                        clus
vv                       SP100 MUTATED SP100 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            11             338
[1] 2 2
[1] FALSE

Clustering(29) Variable = RPL5 MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  RPL5 MUTATED     6   1
  RPL5 WILD-TYPE 309 140
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            449 
  RPL5 MUTATED RPL5 WILD-TYPE 
             1            140 
$`RPL5 MUTATED`
TCGA-49-6742 TCGA-55-7994 TCGA-62-8395 TCGA-78-8662 TCGA-91-6849 TCGA-97-8177 
       14.63        19.82        39.98       110.50         1.15        16.41 
TCGA-NJ-A55R 
       19.82 

$`RPL5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
       15.81        20.19        19.99         4.57        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        10.55        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
       18.67        17.92         5.39        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        59.11 

  RPL5 MUTATED RPL5 WILD-TYPE 
          1.15           0.00 
  RPL5 MUTATED RPL5 WILD-TYPE 
        110.50         223.96 
  RPL5 MUTATED RPL5 WILD-TYPE 
         19.82          17.98 
[1] "1.1 - 110.5 (19.8)" "0.0 - 224.0 (18.0)"
[1] "hr=" "3.4"
D29V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RPL5 MUTATED         0        1        2         0         4          1
  RPL5 WILD-TYPE       4      122      131        46        63         69
                vv
clus             STAGE IIIB STAGE IV
  RPL5 MUTATED            0        0
  RPL5 WILD-TYPE         11       25
D29V3, multiclass
            clus
vv           RPL5 MUTATED RPL5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            131
  STAGE IIA             0             46
  STAGE IIB             4             63
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPL5 MUTATED     1   4   3   0
  RPL5 WILD-TYPE 154 257  40  18
D29V4, multiclass
    clus
vv   RPL5 MUTATED RPL5 WILD-TYPE
  T1            1            154
  T2            4            257
  T3            3             40
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  RPL5 MUTATED     6   1     1
  RPL5 WILD-TYPE 301  88    71
D29V5, multiclass
       clus
vv      RPL5 MUTATED RPL5 WILD-TYPE
  N0               6            301
  N1               1             88
  N2+N3            1             71
[1] 3 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
  RPL5 MUTATED     5   0
  RPL5 WILD-TYPE 322  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      5    0
  RPL5 WILD-TYPE  322   23
   clus
vv  RPL5 MUTATED RPL5 WILD-TYPE
  0            5            322
  1            0             23
[1] 2 2
[1] FALSE
D29V7, binary
                cls
clus               0   1
  RPL5 MUTATED     4   4
  RPL5 WILD-TYPE 255 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      4    4
  RPL5 WILD-TYPE  255  217
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  FEMALE            4            255
  MALE              4            217
[1] 2 2
[1] FALSE
D29V8, continuous
[1] "Remove cluster labels:" "RPL5 MUTATED"          
clus
  RPL5 MUTATED RPL5 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8397 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-93-7348     TCGA-93-8067 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RPL5 MUTATED                            0                                 2
  RPL5 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RPL5 MUTATED                                                    5
  RPL5 WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RPL5 MUTATED                                            0
  RPL5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RPL5 MUTATED                                               0
  RPL5 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RPL5 MUTATED                                0
  RPL5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RPL5 MUTATED                                    0
  RPL5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RPL5 MUTATED                              0                             0
  RPL5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RPL5 MUTATED                                               0
  RPL5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RPL5 MUTATED                              1
  RPL5 WILD-TYPE                            8
D29V9, multiclass
                                                    clus
vv                                                   RPL5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   RPL5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                cls
clus               0   1
  RPL5 MUTATED     0   8
  RPL5 WILD-TYPE  20 452
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      0    8
  RPL5 WILD-TYPE   20  452
     clus
vv    RPL5 MUTATED RPL5 WILD-TYPE
  NO             0             20
  YES            8            452
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, continuous
[1] "Remove cluster labels:" "RPL5 MUTATED"          
clus
  RPL5 MUTATED RPL5 WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     TCGA-44-3396 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-5644 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6147 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     TCGA-44-6776 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7661     TCGA-44-7662     TCGA-44-7667 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7670     TCGA-44-7672     TCGA-44-8117 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-1592     TCGA-55-1595     TCGA-55-5899     TCGA-55-6642 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-6712     TCGA-55-6971     TCGA-55-7227     TCGA-55-7283 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7728     TCGA-55-7907 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7914     TCGA-55-8089 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8615     TCGA-55-8620     TCGA-55-8621 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A493     TCGA-55-A494 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-62-8398     TCGA-64-1677     TCGA-64-1681     TCGA-64-5774 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-7761     TCGA-69-7763     TCGA-69-7764     TCGA-69-7765 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-7979     TCGA-69-8253     TCGA-69-8255 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-A59K     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4675     TCGA-73-4676 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-73-7498     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7145     TCGA-78-7146     TCGA-78-7147 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7148     TCGA-78-7149     TCGA-78-7150     TCGA-78-7152 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7153     TCGA-78-7154     TCGA-78-7155     TCGA-78-7156 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7158     TCGA-78-7159     TCGA-78-7160     TCGA-78-7161 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7162     TCGA-78-7163     TCGA-78-7166     TCGA-78-7167 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7542     TCGA-78-7633     TCGA-78-8640 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-8648     TCGA-78-8655     TCGA-78-8660     TCGA-80-5607 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-80-5608     TCGA-83-5908     TCGA-86-6851     TCGA-86-7711 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-8054     TCGA-86-8055 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8281 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8669     TCGA-86-8673 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-91-6829     TCGA-91-6830 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-91-6836     TCGA-91-6840     TCGA-91-8499     TCGA-91-A4BC 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  RPL5 MUTATED     5   0   0   0
  RPL5 WILD-TYPE 305  11   4  25
D29V13, multiclass
    clus
vv   RPL5 MUTATED RPL5 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPL5 MUTATED                                  0     0
  RPL5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPL5 MUTATED                           1     5
  RPL5 WILD-TYPE                        28   372
D29V14, multiclass
                                  clus
vv                                 RPL5 MUTATED RPL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                cls
clus               0   1
  RPL5 MUTATED     0   6
  RPL5 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      0    6
  RPL5 WILD-TYPE    6  343
                        clus
vv                       RPL5 MUTATED RPL5 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(30) Variable = AACS MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  AACS MUTATED    11   6
  AACS WILD-TYPE 304 135
  AACS MUTATED AACS WILD-TYPE 
            17            439 
  AACS MUTATED AACS WILD-TYPE 
             6            135 
$`AACS MUTATED`
TCGA-05-4398 TCGA-05-5428 TCGA-35-5375 TCGA-44-3396 TCGA-44-5644 TCGA-44-6777 
       47.05        22.03         8.68        37.15        28.37        32.45 
TCGA-44-7661 TCGA-44-8120 TCGA-49-4487 TCGA-50-5930 TCGA-50-8457 TCGA-55-8089 
       12.03         8.55        28.11         9.27        25.61         3.29 
TCGA-62-A46P TCGA-62-A46R TCGA-69-7979 TCGA-78-7537 TCGA-NJ-A4YQ 
       19.53        56.71         2.93        53.33        29.13 

$`AACS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3398 
        4.37        46.98        13.15        24.36        42.77        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
       34.06         6.25        26.56        33.30        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       63.72        61.28        16.44        14.60        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        10.13         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  AACS MUTATED AACS WILD-TYPE 
          2.93           0.00 
  AACS MUTATED AACS WILD-TYPE 
         56.71         223.96 
  AACS MUTATED AACS WILD-TYPE 
         25.61          17.75 
[1] "2.9 - 56.7 (25.6)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D30V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AACS MUTATED         0        5        8         1         0          3
  AACS WILD-TYPE       4      118      125        45        67         67
                vv
clus             STAGE IIIB STAGE IV
  AACS MUTATED            1        0
  AACS WILD-TYPE         10       25
D30V3, multiclass
            clus
vv           AACS MUTATED AACS WILD-TYPE
  STAGE I               0              4
  STAGE IA              5            118
  STAGE IB              8            125
  STAGE IIA             1             45
  STAGE IIB             0             67
  STAGE IIIA            3             67
  STAGE IIIB            1             10
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AACS MUTATED     6  11   0   1
  AACS WILD-TYPE 149 250  43  17
D30V4, multiclass
    clus
vv   AACS MUTATED AACS WILD-TYPE
  T1            6            149
  T2           11            250
  T3            0             43
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  AACS MUTATED    11   1     4
  AACS WILD-TYPE 296  88    68
D30V5, multiclass
       clus
vv      AACS MUTATED AACS WILD-TYPE
  N0              11            296
  N1               1             88
  N2+N3            4             68
[1] 3 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
  AACS MUTATED    15   0
  AACS WILD-TYPE 312  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  AACS MUTATED     15    0
  AACS WILD-TYPE  312   23
   clus
vv  AACS MUTATED AACS WILD-TYPE
  0           15            312
  1            0             23
[1] 2 2
[1] FALSE
D30V7, binary
                cls
clus               0   1
  AACS MUTATED    10   8
  AACS WILD-TYPE 249 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  AACS MUTATED     10    8
  AACS WILD-TYPE  249  213
        clus
vv       AACS MUTATED AACS WILD-TYPE
  FEMALE           10            249
  MALE              8            213
[1] 2 2
[1] FALSE
D30V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AACS MUTATED                            1                                 7
  AACS WILD-TYPE                         17                                95
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AACS MUTATED                                                   10
  AACS WILD-TYPE                                                284
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AACS MUTATED                                            0
  AACS WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AACS MUTATED                                               0
  AACS WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  AACS MUTATED                                0
  AACS WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  AACS MUTATED                                    0
  AACS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  AACS MUTATED                              0                             0
  AACS WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AACS MUTATED                                               0
  AACS WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  AACS MUTATED                              0
  AACS WILD-TYPE                            9
D30V9, multiclass
                                                    clus
vv                                                   AACS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   AACS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                cls
clus               0   1
  AACS MUTATED     2  16
  AACS WILD-TYPE  18 444
[1] "tbl2"
                cls
clus             [,1] [,2]
  AACS MUTATED      2   16
  AACS WILD-TYPE   18  444
     clus
vv    AACS MUTATED AACS WILD-TYPE
  NO             2             18
  YES           16            444
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, continuous
                vv
clus              R0  R1  R2  RX
  AACS MUTATED     9   0   0   1
  AACS WILD-TYPE 301  11   4  24
D30V13, multiclass
    clus
vv   AACS MUTATED AACS WILD-TYPE
  R0            9            301
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AACS MUTATED                                  0     0
  AACS WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AACS MUTATED                           2    13
  AACS WILD-TYPE                        27   364
D30V14, multiclass
                                  clus
vv                                 AACS MUTATED AACS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                      13            364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                cls
clus               0   1
  AACS MUTATED     0  14
  AACS WILD-TYPE   6 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  AACS MUTATED      0   14
  AACS WILD-TYPE    6  335
                        clus
vv                       AACS MUTATED AACS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           14            335
[1] 2 2
[1] FALSE

Clustering(31) Variable = ITGBL1 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  ITGBL1 MUTATED    12   7
  ITGBL1 WILD-TYPE 303 134
  ITGBL1 MUTATED ITGBL1 WILD-TYPE 
              19              437 
  ITGBL1 MUTATED ITGBL1 WILD-TYPE 
               7              134 
$`ITGBL1 MUTATED`
TCGA-05-4382 TCGA-05-4418 TCGA-44-4112 TCGA-50-5045 TCGA-55-6968 TCGA-55-7907 
       19.96         9.01        26.56        71.47        42.51         0.53 
TCGA-55-8506 TCGA-55-8615 TCGA-55-8620 TCGA-62-8398 TCGA-69-7980 TCGA-78-7539 
        0.36         0.49         2.17        14.60        12.56        10.75 
TCGA-86-6851 TCGA-86-8672 TCGA-91-6830 TCGA-91-6848 TCGA-97-A4M7 TCGA-MN-A4N1 
        5.88         0.62         1.97         7.36        20.68        27.19 
TCGA-MP-A4T4 
       86.04 

$`ITGBL1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24        34.06         6.25        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       48.62         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
       17.62         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       20.19        19.99         4.57        39.98        42.38        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       30.84        27.58        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62        41.36        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       19.76        20.52        17.75        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ITGBL1 MUTATED ITGBL1 WILD-TYPE 
            0.36             0.00 
  ITGBL1 MUTATED ITGBL1 WILD-TYPE 
           86.04           223.96 
  ITGBL1 MUTATED ITGBL1 WILD-TYPE 
           10.75            18.18 
[1] "0.4 - 86.0 (10.8)"  "0.0 - 224.0 (18.2)"
[1] "hr=" "1.4"
D31V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ITGBL1 MUTATED         1        2        2         5         3          4
  ITGBL1 WILD-TYPE       3      121      131        41        64         66
                  vv
clus               STAGE IIIB STAGE IV
  ITGBL1 MUTATED            0        2
  ITGBL1 WILD-TYPE         11       23
D31V3, multiclass
            clus
vv           ITGBL1 MUTATED ITGBL1 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                2              121
  STAGE IB                2              131
  STAGE IIA               5               41
  STAGE IIB               3               64
  STAGE IIIA              4               66
  STAGE IIIB              0               11
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ITGBL1 MUTATED     6   9   4   0
  ITGBL1 WILD-TYPE 149 252  39  18
D31V4, multiclass
    clus
vv   ITGBL1 MUTATED ITGBL1 WILD-TYPE
  T1              6              149
  T2              9              252
  T3              4               39
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ITGBL1 MUTATED     8   7     4
  ITGBL1 WILD-TYPE 299  82    68
D31V5, multiclass
       clus
vv      ITGBL1 MUTATED ITGBL1 WILD-TYPE
  N0                 8              299
  N1                 7               82
  N2+N3              4               68
[1] 3 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
  ITGBL1 MUTATED    12   2
  ITGBL1 WILD-TYPE 315  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGBL1 MUTATED     12    2
  ITGBL1 WILD-TYPE  315   21
   clus
vv  ITGBL1 MUTATED ITGBL1 WILD-TYPE
  0             12              315
  1              2               21
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                 0   1
  ITGBL1 MUTATED     8  11
  ITGBL1 WILD-TYPE 251 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGBL1 MUTATED      8   11
  ITGBL1 WILD-TYPE  251  210
        clus
vv       ITGBL1 MUTATED ITGBL1 WILD-TYPE
  FEMALE              8              251
  MALE               11              210
[1] 2 2
[1] FALSE
D31V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ITGBL1 MUTATED                            0                                 6
  ITGBL1 WILD-TYPE                         18                                96
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ITGBL1 MUTATED                                                   13
  ITGBL1 WILD-TYPE                                                281
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ITGBL1 MUTATED                                            0
  ITGBL1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ITGBL1 MUTATED                                               0
  ITGBL1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ITGBL1 MUTATED                                0
  ITGBL1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ITGBL1 MUTATED                                    0
  ITGBL1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ITGBL1 MUTATED                              0                             0
  ITGBL1 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ITGBL1 MUTATED                                               0
  ITGBL1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ITGBL1 MUTATED                              0
  ITGBL1 WILD-TYPE                            9
D31V9, multiclass
                                                    clus
vv                                                   ITGBL1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ITGBL1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                  cls
clus                 0   1
  ITGBL1 MUTATED     1  18
  ITGBL1 WILD-TYPE  19 442
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGBL1 MUTATED      1   18
  ITGBL1 WILD-TYPE   19  442
     clus
vv    ITGBL1 MUTATED ITGBL1 WILD-TYPE
  NO               1               19
  YES             18              442
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, continuous
                  vv
clus                R0  R1  R2  RX
  ITGBL1 MUTATED    13   0   0   0
  ITGBL1 WILD-TYPE 297  11   4  25
D31V13, multiclass
    clus
vv   ITGBL1 MUTATED ITGBL1 WILD-TYPE
  R0             13              297
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGBL1 MUTATED                                  0     0
  ITGBL1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ITGBL1 MUTATED                           2    15
  ITGBL1 WILD-TYPE                        27   362
D31V14, multiclass
                                  clus
vv                                 ITGBL1 MUTATED ITGBL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        15              362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, binary
                  cls
clus                 0   1
  ITGBL1 MUTATED     0  15
  ITGBL1 WILD-TYPE   6 334
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGBL1 MUTATED      0   15
  ITGBL1 WILD-TYPE    6  334
                        clus
vv                       ITGBL1 MUTATED ITGBL1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             15              334
[1] 2 2
[1] FALSE

Clustering(32) Variable = NLRP6 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  NLRP6 MUTATED     7   2
  NLRP6 WILD-TYPE 308 139
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              9             447 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             139 
$`NLRP6 MUTATED`
TCGA-05-4420 TCGA-44-7660 TCGA-55-6642 TCGA-55-7907 TCGA-55-8094 TCGA-86-7714 
       29.98        19.46        32.65         0.53         0.13        20.55 
TCGA-97-A4M7 TCGA-99-8025 TCGA-MP-A4SV 
       20.68        34.85        86.14 

$`NLRP6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        14.60        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
        9.21        23.05        48.62         2.86         0.07         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        13.87        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        24.56        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
           0.13            0.00 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          86.14          223.96 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          20.68           17.75 
[1] "0.1 - 86.1 (20.7)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.7"
D32V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NLRP6 MUTATED         0        1        5         1         0          2
  NLRP6 WILD-TYPE       4      122      128        45        67         68
                 vv
clus              STAGE IIIB STAGE IV
  NLRP6 MUTATED            0        1
  NLRP6 WILD-TYPE         11       24
D32V3, multiclass
            clus
vv           NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               5             128
  STAGE IIA              1              45
  STAGE IIB              0              67
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRP6 MUTATED     2   7   1   0
  NLRP6 WILD-TYPE 153 254  42  18
D32V4, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  T1             2             153
  T2             7             254
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  NLRP6 MUTATED     7   1     2
  NLRP6 WILD-TYPE 300  88    70
D32V5, multiclass
       clus
vv      NLRP6 MUTATED NLRP6 WILD-TYPE
  N0                7             300
  N1                1              88
  N2+N3             2              70
[1] 3 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
  NLRP6 MUTATED     6   1
  NLRP6 WILD-TYPE 321  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      6    1
  NLRP6 WILD-TYPE  321   22
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             6             321
  1             1              22
[1] 2 2
[1] FALSE
D32V7, binary
                 cls
clus                0   1
  NLRP6 MUTATED     3   7
  NLRP6 WILD-TYPE 256 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      3    7
  NLRP6 WILD-TYPE  256  214
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             3             256
  MALE               7             214
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NLRP6 MUTATED                            0                                 3
  NLRP6 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NLRP6 MUTATED                                                    7
  NLRP6 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NLRP6 MUTATED                                            0
  NLRP6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NLRP6 MUTATED                                               0
  NLRP6 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NLRP6 MUTATED                                0
  NLRP6 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NLRP6 MUTATED                                    0
  NLRP6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NLRP6 MUTATED                              0                             0
  NLRP6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NLRP6 MUTATED                                               0
  NLRP6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NLRP6 MUTATED                              0
  NLRP6 WILD-TYPE                            9
D32V9, multiclass
                                                    clus
vv                                                   NLRP6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NLRP6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0  10
  NLRP6 WILD-TYPE  20 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0   10
  NLRP6 WILD-TYPE   20  450
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              0              20
  YES            10             450
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, continuous
                 vv
clus               R0  R1  R2  RX
  NLRP6 MUTATED     9   0   0   0
  NLRP6 WILD-TYPE 301  11   4  25
D32V13, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRP6 MUTATED                                  0     0
  NLRP6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NLRP6 MUTATED                           2     5
  NLRP6 WILD-TYPE                        27   372
D32V14, multiclass
                                  clus
vv                                 NLRP6 MUTATED NLRP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   6
  NLRP6 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    6
  NLRP6 WILD-TYPE    6  343
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(33) Variable = STIM1 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  STIM1 MUTATED     9   0
  STIM1 WILD-TYPE 306 141
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             447 
  STIM1 MUTATED STIM1 WILD-TYPE 
              0             141 
$`STIM1 MUTATED`
TCGA-05-4427 TCGA-35-4123 TCGA-44-2656 TCGA-55-8510 TCGA-69-7979 TCGA-78-8640 
       26.01         5.98        46.98        17.72         2.93       214.62 
TCGA-86-8673 TCGA-95-7043 TCGA-NJ-A4YG 
       14.96         1.22        62.60 

$`STIM1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
        0.76         0.95         0.36         0.26         0.49         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.30        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        10.55        32.68        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  STIM1 MUTATED STIM1 WILD-TYPE 
           1.22            0.00 
  STIM1 MUTATED STIM1 WILD-TYPE 
         214.62          223.96 
  STIM1 MUTATED STIM1 WILD-TYPE 
          17.72           18.08 
[1] "1.2 - 214.6 (17.7)" "0.0 - 224.0 (18.1)"
[1] "hr="     "2.7e+07"
D33V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STIM1 MUTATED         0        2        5         1         1          0
  STIM1 WILD-TYPE       4      121      128        45        66         70
                 vv
clus              STAGE IIIB STAGE IV
  STIM1 MUTATED            0        0
  STIM1 WILD-TYPE         11       25
D33V3, multiclass
            clus
vv           STIM1 MUTATED STIM1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               5             128
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STIM1 MUTATED     3   6   0   0
  STIM1 WILD-TYPE 152 255  43  18
D33V4, multiclass
    clus
vv   STIM1 MUTATED STIM1 WILD-TYPE
  T1             3             152
  T2             6             255
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  STIM1 MUTATED     7   2     0
  STIM1 WILD-TYPE 300  87    72
D33V5, multiclass
       clus
vv      STIM1 MUTATED STIM1 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             0              72
[1] 3 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
  STIM1 MUTATED     6   0
  STIM1 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      6    0
  STIM1 WILD-TYPE  321   23
   clus
vv  STIM1 MUTATED STIM1 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus                0   1
  STIM1 MUTATED     4   5
  STIM1 WILD-TYPE 255 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      4    5
  STIM1 WILD-TYPE  255  216
        clus
vv       STIM1 MUTATED STIM1 WILD-TYPE
  FEMALE             4             255
  MALE               5             216
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "STIM1 MUTATED"         
clus
  STIM1 MUTATED STIM1 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-5375      TCGA-53-A4EZ      TCGA-55-7283 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STIM1 MUTATED                            1                                 2
  STIM1 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STIM1 MUTATED                                                    5
  STIM1 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STIM1 MUTATED                                            0
  STIM1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STIM1 MUTATED                                               1
  STIM1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STIM1 MUTATED                                0
  STIM1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STIM1 MUTATED                                    0
  STIM1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STIM1 MUTATED                              0                             0
  STIM1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STIM1 MUTATED                                               0
  STIM1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STIM1 MUTATED                              0
  STIM1 WILD-TYPE                            9
D33V9, multiclass
                                                    clus
vv                                                   STIM1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STIM1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                 cls
clus                0   1
  STIM1 MUTATED     0   9
  STIM1 WILD-TYPE  20 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      0    9
  STIM1 WILD-TYPE   20  451
     clus
vv    STIM1 MUTATED STIM1 WILD-TYPE
  NO              0              20
  YES             9             451
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, continuous
                 vv
clus               R0  R1  R2  RX
  STIM1 MUTATED     5   0   0   0
  STIM1 WILD-TYPE 305  11   4  25
D33V13, multiclass
    clus
vv   STIM1 MUTATED STIM1 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STIM1 MUTATED                                  0     0
  STIM1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STIM1 MUTATED                           0     7
  STIM1 WILD-TYPE                        29   370
D33V14, multiclass
                                  clus
vv                                 STIM1 MUTATED STIM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                 cls
clus                0   1
  STIM1 MUTATED     0   6
  STIM1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      0    6
  STIM1 WILD-TYPE    6  343
                        clus
vv                       STIM1 MUTATED STIM1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(34) Variable = NCKAP1L MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                 0   1
  NCKAP1L MUTATED    12   7
  NCKAP1L WILD-TYPE 303 134
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               437 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                7               134 
$`NCKAP1L MUTATED`
TCGA-05-4396 TCGA-05-4432 TCGA-44-7667 TCGA-44-7670 TCGA-50-5930 TCGA-50-5946 
        9.96        25.02        36.07        29.00         9.27        22.55 
TCGA-55-1592 TCGA-55-7907 TCGA-55-8092 TCGA-67-3771 TCGA-73-4658 TCGA-78-7162 
       23.05         0.53         5.06        20.05        52.60       104.19 
TCGA-78-7536 TCGA-78-7633 TCGA-95-7039 TCGA-95-A4VK TCGA-99-8028 TCGA-L9-A444 
        8.02        32.68         1.12        21.40        36.76         0.20 
TCGA-MN-A4N4 
       38.63 

$`NCKAP1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       16.44        14.60        19.46        12.03         7.17        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.22        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
        8.45        15.12        18.64        29.03        25.12        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94         9.21        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       64.90        22.29         7.07       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20        53.33        10.75        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29         2.76        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
              0.2               0.0 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
           104.19            223.96 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
            22.55             17.75 
[1] "0.2 - 104.2 (22.6)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D34V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NCKAP1L MUTATED         0        8        1         2         4          3
  NCKAP1L WILD-TYPE       4      115      132        44        63         67
                   vv
clus                STAGE IIIB STAGE IV
  NCKAP1L MUTATED            1        0
  NCKAP1L WILD-TYPE         10       25
D34V3, multiclass
            clus
vv           NCKAP1L MUTATED NCKAP1L WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 8               115
  STAGE IB                 1               132
  STAGE IIA                2                44
  STAGE IIB                4                63
  STAGE IIIA               3                67
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NCKAP1L MUTATED     7   8   3   1
  NCKAP1L WILD-TYPE 148 253  40  17
D34V4, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  T1               7               148
  T2               8               253
  T3               3                40
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  NCKAP1L MUTATED    12   4     3
  NCKAP1L WILD-TYPE 295  85    69
D34V5, multiclass
       clus
vv      NCKAP1L MUTATED NCKAP1L WILD-TYPE
  N0                 12               295
  N1                  4                85
  N2+N3               3                69
[1] 3 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
  NCKAP1L MUTATED    13   0
  NCKAP1L WILD-TYPE 314  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED     13    0
  NCKAP1L WILD-TYPE  314   23
   clus
vv  NCKAP1L MUTATED NCKAP1L WILD-TYPE
  0              13               314
  1               0                23
[1] 2 2
[1] FALSE
D34V7, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     8  11
  NCKAP1L WILD-TYPE 251 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      8   11
  NCKAP1L WILD-TYPE  251  210
        clus
vv       NCKAP1L MUTATED NCKAP1L WILD-TYPE
  FEMALE               8               251
  MALE                11               210
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "NCKAP1L MUTATED"       
clus
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-93-7348        TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-99-7458        TCGA-MN-A4N1        TCGA-MN-A4N5 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  NCKAP1L MUTATED                            0
  NCKAP1L WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  NCKAP1L MUTATED                                   8
  NCKAP1L WILD-TYPE                                94
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NCKAP1L MUTATED                                                   11
  NCKAP1L WILD-TYPE                                                283
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NCKAP1L MUTATED                                            0
  NCKAP1L WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NCKAP1L MUTATED                                               0
  NCKAP1L WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  NCKAP1L MUTATED                                0
  NCKAP1L WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  NCKAP1L MUTATED                                    0
  NCKAP1L WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NCKAP1L MUTATED                              0                             0
  NCKAP1L WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NCKAP1L MUTATED                                               0
  NCKAP1L WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  NCKAP1L MUTATED                              0
  NCKAP1L WILD-TYPE                            9
D34V9, multiclass
                                                    clus
vv                                                   NCKAP1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   NCKAP1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     2  17
  NCKAP1L WILD-TYPE  18 443
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      2   17
  NCKAP1L WILD-TYPE   18  443
     clus
vv    NCKAP1L MUTATED NCKAP1L WILD-TYPE
  NO                2                18
  YES              17               443
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, continuous
                   vv
clus                 R0  R1  R2  RX
  NCKAP1L MUTATED    13   0   0   1
  NCKAP1L WILD-TYPE 297  11   4  24
D34V13, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  R0              13               297
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCKAP1L MUTATED                                  0     0
  NCKAP1L WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NCKAP1L MUTATED                           2    15
  NCKAP1L WILD-TYPE                        27   362
D34V14, multiclass
                                  clus
vv                                 NCKAP1L MUTATED NCKAP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         15               362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     1  12
  NCKAP1L WILD-TYPE   5 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      1   12
  NCKAP1L WILD-TYPE    5  337
                        clus
vv                       NCKAP1L MUTATED NCKAP1L WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              12               337
[1] 2 2
[1] FALSE

Clustering(35) Variable = CTNNB1 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    13   4
  CTNNB1 WILD-TYPE 302 137
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              17              439 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4              137 
$`CTNNB1 MUTATED`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4422 TCGA-05-4425 TCGA-44-4112 TCGA-44-A47A 
       14.01        45.01        12.00        21.99        26.56        15.32 
TCGA-55-8085 TCGA-55-A48Y TCGA-62-A46V TCGA-62-A470 TCGA-67-3771 TCGA-69-7979 
       29.72        20.71        72.30        39.25        20.05         2.93 
TCGA-78-7153 TCGA-78-7158 TCGA-86-8280 TCGA-97-8171 TCGA-MP-A4SV 
       24.99         5.88        23.05        18.67        86.14 

$`CTNNB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
       14.96         9.01        29.98        30.02        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06         6.25        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       23.64        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 
        6.48        17.65         6.15        19.82         0.16        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       54.35        67.96        13.61        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.30        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50        32.09        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
        3.81         0.20        27.19        38.63         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            2.93             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           86.14           223.96 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           21.99            17.72 
[1] "2.9 - 86.1 (22.0)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "1.6"
D35V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CTNNB1 MUTATED         0        3        9         2         0          2
  CTNNB1 WILD-TYPE       4      120      124        44        67         68
                  vv
clus               STAGE IIIB STAGE IV
  CTNNB1 MUTATED            1        2
  CTNNB1 WILD-TYPE         10       23
D35V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                9              124
  STAGE IIA               2               44
  STAGE IIB               0               67
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of 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     3  14   1   1
  CTNNB1 WILD-TYPE 152 247  42  17
D35V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              3              152
  T2             14              247
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  CTNNB1 MUTATED    15   0     4
  CTNNB1 WILD-TYPE 292  89    68
D35V5, multiclass
       clus
vv      CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0                15              292
  N1                 0               89
  N2+N3              4               68
[1] 3 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
  CTNNB1 MUTATED    15   2
  CTNNB1 WILD-TYPE 312  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     15    2
  CTNNB1 WILD-TYPE  312   21
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             15              312
  1              2               21
[1] 2 2
[1] FALSE
D35V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    10   9
  CTNNB1 WILD-TYPE 249 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     10    9
  CTNNB1 WILD-TYPE  249  212
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             10              249
  MALE                9              212
[1] 2 2
[1] FALSE
D35V8, continuous
[1] "Remove cluster labels:" "CTNNB1 MUTATED"        
clus
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46Y       TCGA-62-A471       TCGA-62-A472 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5778       TCGA-69-7974 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4676 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CTNNB1 MUTATED                            2                                 7
  CTNNB1 WILD-TYPE                         16                                95
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CTNNB1 MUTATED                                                    7
  CTNNB1 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CTNNB1 MUTATED                                            0
  CTNNB1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CTNNB1 MUTATED                                               1
  CTNNB1 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CTNNB1 MUTATED                                0
  CTNNB1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CTNNB1 MUTATED                                    0
  CTNNB1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CTNNB1 MUTATED                              0                             2
  CTNNB1 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CTNNB1 MUTATED                                               0
  CTNNB1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CTNNB1 MUTATED                              0
  CTNNB1 WILD-TYPE                            9
D35V9, multiclass
                                                    clus
vv                                                   CTNNB1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CTNNB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0  19
  CTNNB1 WILD-TYPE  20 441
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0   19
  CTNNB1 WILD-TYPE   20  441
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               0               20
  YES             19              441
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, continuous
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    14   2   0   1
  CTNNB1 WILD-TYPE 296   9   4  24
D35V13, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             14              296
  R1              2                9
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  0     1
  CTNNB1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           1    11
  CTNNB1 WILD-TYPE                        28   366
D35V14, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        11              366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0  11
  CTNNB1 WILD-TYPE   6 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0   11
  CTNNB1 WILD-TYPE    6  338
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(36) Variable = PLEKHB2 MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                 0   1
  PLEKHB2 MUTATED     6   3
  PLEKHB2 WILD-TYPE 309 138
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                9               447 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                3               138 
$`PLEKHB2 MUTATED`
TCGA-44-7662 TCGA-49-6767 TCGA-50-5941 TCGA-55-8203 TCGA-55-8302 TCGA-55-A4DF 
        7.17        22.26        18.64        17.98         0.76        20.19 
TCGA-78-7220 TCGA-MP-A4SV TCGA-NJ-A55R 
       26.53        86.14        19.82 

$`PLEKHB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       40.60        78.67        21.47         8.45        15.12        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
       19.73         5.06         0.13        23.64        15.65         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.51         2.17        22.16        15.42         1.45         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       20.58        19.59         0.92        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63         2.76        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.26         0.43        59.11 

  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
             0.76              0.00 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
            86.14            223.96 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
            19.82             17.75 
[1] "0.8 - 86.1 (19.8)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1"  
D36V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PLEKHB2 MUTATED         0        2        4         0         1          2
  PLEKHB2 WILD-TYPE       4      121      129        46        66         68
                   vv
clus                STAGE IIIB STAGE IV
  PLEKHB2 MUTATED            0        0
  PLEKHB2 WILD-TYPE         11       25
D36V3, multiclass
            clus
vv           PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 4               129
  STAGE IIA                0                46
  STAGE IIB                1                66
  STAGE IIIA               2                68
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHB2 MUTATED     3   5   1   0
  PLEKHB2 WILD-TYPE 152 256  42  18
D36V4, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  T1               3               152
  T2               5               256
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  PLEKHB2 MUTATED     7   0     2
  PLEKHB2 WILD-TYPE 300  89    70
D36V5, multiclass
       clus
vv      PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  N0                  7               300
  N1                  0                89
  N2+N3               2                70
[1] 3 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
  PLEKHB2 MUTATED     3   0
  PLEKHB2 WILD-TYPE 324  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      3    0
  PLEKHB2 WILD-TYPE  324   23
   clus
vv  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  0               3               324
  1               0                23
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     4   5
  PLEKHB2 WILD-TYPE 255 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      4    5
  PLEKHB2 WILD-TYPE  255  216
        clus
vv       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  FEMALE               4               255
  MALE                 5               216
[1] 2 2
[1] FALSE
D36V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PLEKHB2 MUTATED                            0
  PLEKHB2 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PLEKHB2 MUTATED                                   1
  PLEKHB2 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PLEKHB2 MUTATED                                                    8
  PLEKHB2 WILD-TYPE                                                286
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PLEKHB2 MUTATED                                            0
  PLEKHB2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PLEKHB2 MUTATED                                               0
  PLEKHB2 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  PLEKHB2 MUTATED                                0
  PLEKHB2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  PLEKHB2 MUTATED                                    0
  PLEKHB2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PLEKHB2 MUTATED                              0                             0
  PLEKHB2 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PLEKHB2 MUTATED                                               0
  PLEKHB2 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  PLEKHB2 MUTATED                              0
  PLEKHB2 WILD-TYPE                            9
D36V9, multiclass
                                                    clus
vv                                                   PLEKHB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   PLEKHB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     1   8
  PLEKHB2 WILD-TYPE  19 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      1    8
  PLEKHB2 WILD-TYPE   19  452
     clus
vv    PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  NO                1                19
  YES               8               452
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, continuous
                   vv
clus                 R0  R1  R2  RX
  PLEKHB2 MUTATED     6   0   0   0
  PLEKHB2 WILD-TYPE 304  11   4  25
D36V13, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHB2 MUTATED                                  0     0
  PLEKHB2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHB2 MUTATED                           0     8
  PLEKHB2 WILD-TYPE                        29   369
D36V14, multiclass
                                  clus
vv                                 PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          8               369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     0   4
  PLEKHB2 WILD-TYPE   6 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      0    4
  PLEKHB2 WILD-TYPE    6  345
                        clus
vv                       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               4               345
[1] 2 2
[1] FALSE

Clustering(37) Variable = G3BP1 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  G3BP1 MUTATED     4   3
  G3BP1 WILD-TYPE 311 138
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              7             449 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              3             138 
$`G3BP1 MUTATED`
TCGA-05-4432 TCGA-44-2661 TCGA-49-4486 TCGA-50-5044 TCGA-50-6594 TCGA-53-A4EZ 
       25.02        24.36        76.21        20.52        12.16         9.21 
TCGA-67-3771 
       20.05 

$`G3BP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       14.73        26.30         4.37        46.98        13.15        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       22.55        42.35         3.91        25.55        11.05         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       34.29        30.54        13.94        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       28.47        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  G3BP1 MUTATED G3BP1 WILD-TYPE 
           9.21            0.00 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
          76.21          223.96 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
          20.52           17.92 
[1] "9.2 - 76.2 (20.5)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.2"
D37V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  G3BP1 MUTATED         0        3        0         1         1          2
  G3BP1 WILD-TYPE       4      120      133        45        66         68
                 vv
clus              STAGE IIIB STAGE IV
  G3BP1 MUTATED            1        0
  G3BP1 WILD-TYPE         10       25
D37V3, multiclass
            clus
vv           G3BP1 MUTATED G3BP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               0             133
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             2              68
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  G3BP1 MUTATED     3   2   2   1
  G3BP1 WILD-TYPE 152 259  41  17
D37V4, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  T1             3             152
  T2             2             259
  T3             2              41
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  G3BP1 MUTATED     3   3     2
  G3BP1 WILD-TYPE 304  86    70
D37V5, multiclass
       clus
vv      G3BP1 MUTATED G3BP1 WILD-TYPE
  N0                3             304
  N1                3              86
  N2+N3             2              70
[1] 3 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
  G3BP1 MUTATED     7   0
  G3BP1 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      7    0
  G3BP1 WILD-TYPE  320   23
   clus
vv  G3BP1 MUTATED G3BP1 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D37V7, binary
                 cls
clus                0   1
  G3BP1 MUTATED     5   3
  G3BP1 WILD-TYPE 254 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      5    3
  G3BP1 WILD-TYPE  254  218
        clus
vv       G3BP1 MUTATED G3BP1 WILD-TYPE
  FEMALE             5             254
  MALE               3             218
[1] 2 2
[1] FALSE
D37V8, continuous
[1] "Remove cluster labels:" "G3BP1 MUTATED"         
clus
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-55-7283 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  G3BP1 MUTATED                            1                                 1
  G3BP1 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  G3BP1 MUTATED                                                    5
  G3BP1 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  G3BP1 MUTATED                                            0
  G3BP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  G3BP1 MUTATED                                               0
  G3BP1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  G3BP1 MUTATED                                0
  G3BP1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  G3BP1 MUTATED                                    0
  G3BP1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  G3BP1 MUTATED                              0                             1
  G3BP1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  G3BP1 MUTATED                                               0
  G3BP1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  G3BP1 MUTATED                              0
  G3BP1 WILD-TYPE                            9
D37V9, multiclass
                                                    clus
vv                                                   G3BP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   G3BP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                 cls
clus                0   1
  G3BP1 MUTATED     0   8
  G3BP1 WILD-TYPE  20 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      0    8
  G3BP1 WILD-TYPE   20  452
     clus
vv    G3BP1 MUTATED G3BP1 WILD-TYPE
  NO              0              20
  YES             8             452
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, continuous
[1] "Remove cluster labels:" "G3BP1 MUTATED"         
clus
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              2             255 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4494      TCGA-49-4505      TCGA-53-7624 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-53-7626      TCGA-53-7813      TCGA-55-1592      TCGA-55-1595 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-5899      TCGA-55-6642      TCGA-55-6712      TCGA-55-6971 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7227      TCGA-55-7283      TCGA-55-7570      TCGA-55-7574 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7576      TCGA-55-7724      TCGA-55-7725      TCGA-55-7726 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7728      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8092      TCGA-55-8094 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8096      TCGA-55-8097      TCGA-55-8205      TCGA-55-8299 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8301      TCGA-55-8302      TCGA-55-8506      TCGA-55-8507 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8514      TCGA-55-8615 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-62-8398      TCGA-64-1677 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5774      TCGA-64-5775      TCGA-64-5778 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-5779      TCGA-64-5781      TCGA-69-7761      TCGA-69-7763 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-7764      TCGA-69-7765      TCGA-69-7974      TCGA-69-7979 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-8253      TCGA-69-8255      TCGA-69-A59K      TCGA-73-4659 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-7498      TCGA-75-6214 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-75-7025      TCGA-75-7027      TCGA-75-7031      TCGA-78-7145 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7146      TCGA-78-7147      TCGA-78-7148      TCGA-78-7149 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7150      TCGA-78-7152      TCGA-78-7153      TCGA-78-7154 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7155      TCGA-78-7156      TCGA-78-7158      TCGA-78-7159 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7160      TCGA-78-7161      TCGA-78-7162      TCGA-78-7163 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7166      TCGA-78-7167      TCGA-78-7220      TCGA-78-7535 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7536      TCGA-78-7537      TCGA-78-7539      TCGA-78-7542 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7633      TCGA-78-8640      TCGA-78-8648      TCGA-78-8655 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-8660      TCGA-78-8662      TCGA-80-5607      TCGA-80-5608 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6851      TCGA-86-7711      TCGA-86-7714 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8281      TCGA-86-8358 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8669      TCGA-86-8673      TCGA-86-8674 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-A456      TCGA-91-6829      TCGA-91-6830      TCGA-91-6836 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-91-6840      TCGA-91-6849      TCGA-91-8499      TCGA-91-A4BC 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043      TCGA-95-7562 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-95-7567      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP      TCGA-97-7546 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7941      TCGA-97-8171 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-8172      TCGA-97-8174      TCGA-97-8176      TCGA-97-8179 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7      TCGA-99-7458 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-99-8025      TCGA-99-8028      TCGA-99-8032      TCGA-J2-8194 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4T2 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8      TCGA-MP-A4T9 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE      TCGA-MP-A4TF 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  G3BP1 MUTATED     4   0   1   1
  G3BP1 WILD-TYPE 306  11   3  24
D37V13, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             1               3
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G3BP1 MUTATED                                  0     0
  G3BP1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  G3BP1 MUTATED                           2     4
  G3BP1 WILD-TYPE                        27   373
D37V14, multiclass
                                  clus
vv                                 G3BP1 MUTATED G3BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                 cls
clus                0   1
  G3BP1 MUTATED     1   5
  G3BP1 WILD-TYPE   5 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      1    5
  G3BP1 WILD-TYPE    5  344
                        clus
vv                       G3BP1 MUTATED G3BP1 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(38) Variable = TLR9 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  TLR9 MUTATED     6   4
  TLR9 WILD-TYPE 309 137
  TLR9 MUTATED TLR9 WILD-TYPE 
            10            446 
  TLR9 MUTATED TLR9 WILD-TYPE 
             4            137 
$`TLR9 MUTATED`
TCGA-05-4415 TCGA-44-A4SS TCGA-49-4487 TCGA-55-6969 TCGA-55-8507 TCGA-62-8395 
        2.99        13.64        28.11        40.73         0.26        39.98 
TCGA-67-3771 TCGA-93-A4JO TCGA-95-7562 TCGA-NJ-A4YQ 
       20.05         1.08         2.86        29.13 

$`TLR9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       11.54        13.45        76.21        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.36         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
        4.57        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       28.47        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
       19.82         9.76         4.18         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         1.22        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  TLR9 MUTATED TLR9 WILD-TYPE 
          0.26           0.00 
  TLR9 MUTATED TLR9 WILD-TYPE 
         40.73         223.96 
  TLR9 MUTATED TLR9 WILD-TYPE 
        16.845         18.030 
[1] "0.3 - 40.7 (16.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.8"
D38V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TLR9 MUTATED         0        6        1         1         1          0
  TLR9 WILD-TYPE       4      117      132        45        66         70
                vv
clus             STAGE IIIB STAGE IV
  TLR9 MUTATED            1        0
  TLR9 WILD-TYPE         10       25
D38V3, multiclass
            clus
vv           TLR9 MUTATED TLR9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              1            132
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            1             10
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TLR9 MUTATED     6   2   1   1
  TLR9 WILD-TYPE 149 259  42  17
D38V4, multiclass
    clus
vv   TLR9 MUTATED TLR9 WILD-TYPE
  T1            6            149
  T2            2            259
  T3            1             42
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  TLR9 MUTATED     8   1     1
  TLR9 WILD-TYPE 299  88    71
D38V5, multiclass
       clus
vv      TLR9 MUTATED TLR9 WILD-TYPE
  N0               8            299
  N1               1             88
  N2+N3            1             71
[1] 3 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
  TLR9 MUTATED     8   0
  TLR9 WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      8    0
  TLR9 WILD-TYPE  319   23
   clus
vv  TLR9 MUTATED TLR9 WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D38V7, binary
                cls
clus               0   1
  TLR9 MUTATED     4   6
  TLR9 WILD-TYPE 255 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      4    6
  TLR9 WILD-TYPE  255  215
        clus
vv       TLR9 MUTATED TLR9 WILD-TYPE
  FEMALE            4            255
  MALE              6            215
[1] 2 2
[1] FALSE
D38V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TLR9 MUTATED                            0                                 3
  TLR9 WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TLR9 MUTATED                                                    7
  TLR9 WILD-TYPE                                                287
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TLR9 MUTATED                                            0
  TLR9 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TLR9 MUTATED                                               0
  TLR9 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  TLR9 MUTATED                                0
  TLR9 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  TLR9 MUTATED                                    0
  TLR9 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TLR9 MUTATED                              0                             0
  TLR9 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TLR9 MUTATED                                               0
  TLR9 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  TLR9 MUTATED                              0
  TLR9 WILD-TYPE                            9
D38V9, multiclass
                                                    clus
vv                                                   TLR9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   TLR9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                cls
clus               0   1
  TLR9 MUTATED     0  10
  TLR9 WILD-TYPE  20 450
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      0   10
  TLR9 WILD-TYPE   20  450
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  NO             0             20
  YES           10            450
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, continuous
                vv
clus              R0  R1  R2  RX
  TLR9 MUTATED     5   0   0   3
  TLR9 WILD-TYPE 305  11   4  22
D38V13, multiclass
    clus
vv   TLR9 MUTATED TLR9 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TLR9 MUTATED                                  0     0
  TLR9 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TLR9 MUTATED                           2     7
  TLR9 WILD-TYPE                        27   370
D38V14, multiclass
                                  clus
vv                                 TLR9 MUTATED TLR9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                cls
clus               0   1
  TLR9 MUTATED     0   8
  TLR9 WILD-TYPE   6 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      0    8
  TLR9 WILD-TYPE    6  341
                        clus
vv                       TLR9 MUTATED TLR9 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(39) Variable = PDE6A MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  PDE6A MUTATED    11   5
  PDE6A WILD-TYPE 304 136
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             440 
  PDE6A MUTATED PDE6A WILD-TYPE 
              5             136 
$`PDE6A MUTATED`
TCGA-05-4382 TCGA-44-5644 TCGA-53-7624 TCGA-55-6642 TCGA-55-6972 TCGA-55-8299 
       19.96        28.37        34.29        32.65        48.49        15.42 
TCGA-55-8507 TCGA-55-A4DG TCGA-62-A46O TCGA-67-3771 TCGA-73-4659 TCGA-73-4668 
        0.26        19.99        47.80        20.05        23.38        15.35 
TCGA-91-6828 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-NJ-A4YQ 
       10.62        27.19        31.23        29.13 

$`PDE6A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16         1.45         0.76         0.95         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        20.19         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
        0.10        52.60        29.98        26.30         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       13.32        17.62        13.64        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 
       16.44        19.00        14.30         3.81         0.20        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  PDE6A MUTATED PDE6A WILD-TYPE 
           0.26            0.00 
  PDE6A MUTATED PDE6A WILD-TYPE 
          48.49          223.96 
  PDE6A MUTATED PDE6A WILD-TYPE 
         25.285          17.685 
[1] "0.3 - 48.5 (25.3)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "1"  
D39V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PDE6A MUTATED         0        7        5         1         1          1
  PDE6A WILD-TYPE       4      116      128        45        66         69
                 vv
clus              STAGE IIIB STAGE IV
  PDE6A MUTATED            0        1
  PDE6A WILD-TYPE         11       24
D39V3, multiclass
            clus
vv           PDE6A MUTATED PDE6A WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             116
  STAGE IB               5             128
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDE6A MUTATED     7   9   0   0
  PDE6A WILD-TYPE 148 252  43  18
D39V4, multiclass
    clus
vv   PDE6A MUTATED PDE6A WILD-TYPE
  T1             7             148
  T2             9             252
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PDE6A MUTATED    13   2     1
  PDE6A WILD-TYPE 294  87    71
D39V5, multiclass
       clus
vv      PDE6A MUTATED PDE6A WILD-TYPE
  N0               13             294
  N1                2              87
  N2+N3             1              71
[1] 3 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
  PDE6A MUTATED    10   1
  PDE6A WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED     10    1
  PDE6A WILD-TYPE  317   22
   clus
vv  PDE6A MUTATED PDE6A WILD-TYPE
  0            10             317
  1             1              22
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus                0   1
  PDE6A MUTATED     8   8
  PDE6A WILD-TYPE 251 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED      8    8
  PDE6A WILD-TYPE  251  213
        clus
vv       PDE6A MUTATED PDE6A WILD-TYPE
  FEMALE             8             251
  MALE               8             213
[1] 2 2
[1] FALSE
D39V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PDE6A MUTATED                            0                                 1
  PDE6A WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PDE6A MUTATED                                                   13
  PDE6A WILD-TYPE                                                281
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PDE6A MUTATED                                            0
  PDE6A WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PDE6A MUTATED                                               0
  PDE6A WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PDE6A MUTATED                                0
  PDE6A WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PDE6A MUTATED                                    1
  PDE6A WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PDE6A MUTATED                              0                             1
  PDE6A WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PDE6A MUTATED                                               0
  PDE6A WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PDE6A MUTATED                              0
  PDE6A WILD-TYPE                            9
D39V9, multiclass
                                                    clus
vv                                                   PDE6A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PDE6A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                 cls
clus                0   1
  PDE6A MUTATED     0  16
  PDE6A WILD-TYPE  20 444
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED      0   16
  PDE6A WILD-TYPE   20  444
     clus
vv    PDE6A MUTATED PDE6A WILD-TYPE
  NO              0              20
  YES            16             444
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, continuous
                 vv
clus               R0  R1  R2  RX
  PDE6A MUTATED    14   0   0   1
  PDE6A WILD-TYPE 296  11   4  24
D39V13, multiclass
    clus
vv   PDE6A MUTATED PDE6A WILD-TYPE
  R0            14             296
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDE6A MUTATED                                  1     0
  PDE6A WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDE6A MUTATED                           2    12
  PDE6A WILD-TYPE                        27   365
D39V14, multiclass
                                  clus
vv                                 PDE6A MUTATED PDE6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                 cls
clus                0   1
  PDE6A MUTATED     1  13
  PDE6A WILD-TYPE   5 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED      1   13
  PDE6A WILD-TYPE    5  336
                        clus
vv                       PDE6A MUTATED PDE6A WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(40) Variable = DUSP22 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2                0   1
  DUSP22 MUTATED    12   4
  DUSP22 WILD-TYPE 303 137
  DUSP22 MUTATED DUSP22 WILD-TYPE 
              16              440 
  DUSP22 MUTATED DUSP22 WILD-TYPE 
               4              137 
$`DUSP22 MUTATED`
TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-49-6767 TCGA-50-5049 TCGA-55-6968 
       44.61        46.98        13.15        22.26        70.55        42.51 
TCGA-55-8302 TCGA-67-3771 TCGA-69-7765 TCGA-69-7980 TCGA-73-4658 TCGA-78-7539 
        0.76        20.05         5.42        12.56        52.60        10.75 
TCGA-78-7542 TCGA-91-6836 TCGA-95-A4VN TCGA-NJ-A4YQ 
       10.55        13.71        18.18        29.13 

$`DUSP22 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       14.73        26.30         4.37        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07        32.65         0.79        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         1.45         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        2.93        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP 
       15.68        15.65        27.29         2.76        21.40        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  DUSP22 MUTATED DUSP22 WILD-TYPE 
            0.76             0.00 
  DUSP22 MUTATED DUSP22 WILD-TYPE 
           70.55           223.96 
  DUSP22 MUTATED DUSP22 WILD-TYPE 
          19.115           17.950 
[1] "0.8 - 70.5 (19.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.5"
D40V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DUSP22 MUTATED         1        3        7         2         1          0
  DUSP22 WILD-TYPE       3      120      126        44        66         70
                  vv
clus               STAGE IIIB STAGE IV
  DUSP22 MUTATED            0        3
  DUSP22 WILD-TYPE         11       22
D40V3, multiclass
            clus
vv           DUSP22 MUTATED DUSP22 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                3              120
  STAGE IB                7              126
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                3               22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DUSP22 MUTATED     4  11   1   1
  DUSP22 WILD-TYPE 151 250  42  17
D40V4, multiclass
    clus
vv   DUSP22 MUTATED DUSP22 WILD-TYPE
  T1              4              151
  T2             11              250
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  DUSP22 MUTATED    14   2     0
  DUSP22 WILD-TYPE 293  87    72
D40V5, multiclass
       clus
vv      DUSP22 MUTATED DUSP22 WILD-TYPE
  N0                14              293
  N1                 2               87
  N2+N3              0               72
[1] 3 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
  DUSP22 MUTATED    11   2
  DUSP22 WILD-TYPE 316  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP22 MUTATED     11    2
  DUSP22 WILD-TYPE  316   21
   clus
vv  DUSP22 MUTATED DUSP22 WILD-TYPE
  0             11              316
  1              2               21
[1] 2 2
[1] FALSE
D40V7, binary
                  cls
clus                 0   1
  DUSP22 MUTATED     9   8
  DUSP22 WILD-TYPE 250 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP22 MUTATED      9    8
  DUSP22 WILD-TYPE  250  213
        clus
vv       DUSP22 MUTATED DUSP22 WILD-TYPE
  FEMALE              9              250
  MALE                8              213
[1] 2 2
[1] FALSE
D40V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DUSP22 MUTATED                            0                                 2
  DUSP22 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DUSP22 MUTATED                                                   14
  DUSP22 WILD-TYPE                                                280
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DUSP22 MUTATED                                            0
  DUSP22 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DUSP22 MUTATED                                               0
  DUSP22 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  DUSP22 MUTATED                                0
  DUSP22 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  DUSP22 MUTATED                                    0
  DUSP22 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DUSP22 MUTATED                              0                             0
  DUSP22 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DUSP22 MUTATED                                               1
  DUSP22 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  DUSP22 MUTATED                              0
  DUSP22 WILD-TYPE                            9
D40V9, multiclass
                                                    clus
vv                                                   DUSP22 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             14
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   DUSP22 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                  cls
clus                 0   1
  DUSP22 MUTATED     1  16
  DUSP22 WILD-TYPE  19 444
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP22 MUTATED      1   16
  DUSP22 WILD-TYPE   19  444
     clus
vv    DUSP22 MUTATED DUSP22 WILD-TYPE
  NO               1               19
  YES             16              444
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, continuous
                  vv
clus                R0  R1  R2  RX
  DUSP22 MUTATED    10   0   0   1
  DUSP22 WILD-TYPE 300  11   4  24
D40V13, multiclass
    clus
vv   DUSP22 MUTATED DUSP22 WILD-TYPE
  R0             10              300
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP22 MUTATED                                  0     0
  DUSP22 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DUSP22 MUTATED                           3    13
  DUSP22 WILD-TYPE                        26   364
D40V14, multiclass
                                  clus
vv                                 DUSP22 MUTATED DUSP22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                        13              364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                  cls
clus                 0   1
  DUSP22 MUTATED     0  12
  DUSP22 WILD-TYPE   6 337
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP22 MUTATED      0   12
  DUSP22 WILD-TYPE    6  337
                        clus
vv                       DUSP22 MUTATED DUSP22 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             12              337
[1] 2 2
[1] FALSE

Clustering(41) Variable = MMP19 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  MMP19 MUTATED     7   1
  MMP19 WILD-TYPE 308 140
  MMP19 MUTATED MMP19 WILD-TYPE 
              8             448 
  MMP19 MUTATED MMP19 WILD-TYPE 
              1             140 
$`MMP19 MUTATED`
TCGA-44-7667 TCGA-44-A47F TCGA-50-5049 TCGA-55-7574 TCGA-78-7148 TCGA-91-6836 
       36.07        11.08        70.55         3.12        20.58        13.71 
TCGA-91-6848 TCGA-95-A4VN 
        7.36        18.18 

$`MMP19 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 
        1.15         7.99         0.20         0.13         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        19.27        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  MMP19 MUTATED MMP19 WILD-TYPE 
           3.12            0.00 
  MMP19 MUTATED MMP19 WILD-TYPE 
          70.55          223.96 
  MMP19 MUTATED MMP19 WILD-TYPE 
         15.945          18.030 
[1] "3.1 - 70.5 (15.9)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.4"
D41V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MMP19 MUTATED         0        1        3         1         3          1
  MMP19 WILD-TYPE       4      122      130        45        64         69
                 vv
clus              STAGE IIIB STAGE IV
  MMP19 MUTATED            0        0
  MMP19 WILD-TYPE         11       25
D41V3, multiclass
            clus
vv           MMP19 MUTATED MMP19 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              1              45
  STAGE IIB              3              64
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP19 MUTATED     0   8   1   0
  MMP19 WILD-TYPE 155 253  42  18
D41V4, multiclass
    clus
vv   MMP19 MUTATED MMP19 WILD-TYPE
  T1             0             155
  T2             8             253
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  MMP19 MUTATED     5   3     1
  MMP19 WILD-TYPE 302  86    71
D41V5, multiclass
       clus
vv      MMP19 MUTATED MMP19 WILD-TYPE
  N0                5             302
  N1                3              86
  N2+N3             1              71
[1] 3 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
  MMP19 MUTATED     6   0
  MMP19 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED      6    0
  MMP19 WILD-TYPE  321   23
   clus
vv  MMP19 MUTATED MMP19 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus                0   1
  MMP19 MUTATED     4   5
  MMP19 WILD-TYPE 255 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED      4    5
  MMP19 WILD-TYPE  255  216
        clus
vv       MMP19 MUTATED MMP19 WILD-TYPE
  FEMALE             4             255
  MALE               5             216
[1] 2 2
[1] FALSE
D41V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MMP19 MUTATED                            0                                 1
  MMP19 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MMP19 MUTATED                                                    7
  MMP19 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MMP19 MUTATED                                            0
  MMP19 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MMP19 MUTATED                                               0
  MMP19 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MMP19 MUTATED                                0
  MMP19 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MMP19 MUTATED                                    0
  MMP19 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MMP19 MUTATED                              0                             0
  MMP19 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MMP19 MUTATED                                               1
  MMP19 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MMP19 MUTATED                              0
  MMP19 WILD-TYPE                            9
D41V9, multiclass
                                                    clus
vv                                                   MMP19 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MMP19 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                 cls
clus                0   1
  MMP19 MUTATED     2   7
  MMP19 WILD-TYPE  18 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED      2    7
  MMP19 WILD-TYPE   18  453
     clus
vv    MMP19 MUTATED MMP19 WILD-TYPE
  NO              2              18
  YES             7             453
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, continuous
                 vv
clus               R0  R1  R2  RX
  MMP19 MUTATED     3   1   0   0
  MMP19 WILD-TYPE 307  10   4  25
D41V13, multiclass
    clus
vv   MMP19 MUTATED MMP19 WILD-TYPE
  R0             3             307
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP19 MUTATED                                  0     0
  MMP19 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP19 MUTATED                           0     8
  MMP19 WILD-TYPE                        29   369
D41V14, multiclass
                                  clus
vv                                 MMP19 MUTATED MMP19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                 cls
clus                0   1
  MMP19 MUTATED     0   7
  MMP19 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED      0    7
  MMP19 WILD-TYPE    6  342
                        clus
vv                       MMP19 MUTATED MMP19 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(42) Variable = APC MUTATION ANALYSIS
D42V1, survival
               sevent
clus2             0   1
  APC MUTATED    12   8
  APC WILD-TYPE 303 133
  APC MUTATED APC WILD-TYPE 
           20           436 
  APC MUTATED APC WILD-TYPE 
            8           133 
$`APC MUTATED`
TCGA-05-4382 TCGA-05-4397 TCGA-05-4402 TCGA-38-4631 TCGA-44-7661 TCGA-44-A4SS 
       19.96        24.03         8.02        11.64        12.03        13.64 
TCGA-49-4507 TCGA-49-6761 TCGA-50-5049 TCGA-50-5930 TCGA-50-8457 TCGA-55-5899 
        8.81        11.64        70.55         9.27        25.61         2.86 
TCGA-55-8510 TCGA-62-8395 TCGA-69-7978 TCGA-73-4659 TCGA-78-7153 TCGA-78-7220 
       17.72        39.98         2.30        23.38        24.99        26.53 
TCGA-78-8662 TCGA-91-6840 
      110.50        12.23 

$`APC WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
        9.96        47.05        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.08        11.54        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       17.16        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        10.13         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
        0.92        15.81        20.19        19.99         4.57        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01         0.10        52.60        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        13.71        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  APC MUTATED APC WILD-TYPE 
          2.3           0.0 
  APC MUTATED APC WILD-TYPE 
       110.50        223.96 
  APC MUTATED APC WILD-TYPE 
        15.68         18.10 
[1] "2.3 - 110.5 (15.7)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D42V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  APC MUTATED         0        5        6         0         3          5
  APC WILD-TYPE       4      118      127        46        64         65
               vv
clus            STAGE IIIB STAGE IV
  APC MUTATED            0        1
  APC WILD-TYPE         11       24
D42V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I              0             4
  STAGE IA             5           118
  STAGE IB             6           127
  STAGE IIA            0            46
  STAGE IIB            3            64
  STAGE IIIA           5            65
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of 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     5  13   2   0
  APC WILD-TYPE 150 248  41  18
D42V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           5           150
  T2          13           248
  T3           2            41
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  APC MUTATED    11   4     4
  APC WILD-TYPE 296  85    68
D42V5, multiclass
       clus
vv      APC MUTATED APC WILD-TYPE
  N0             11           296
  N1              4            85
  N2+N3           4            68
[1] 3 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
  APC MUTATED    16   1
  APC WILD-TYPE 311  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     16    1
  APC WILD-TYPE  311   22
   clus
vv  APC MUTATED APC WILD-TYPE
  0          16           311
  1           1            22
[1] 2 2
[1] FALSE
D42V7, binary
               cls
clus              0   1
  APC MUTATED    12   8
  APC WILD-TYPE 247 213
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     12    8
  APC WILD-TYPE  247  213
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          12           247
  MALE             8           213
[1] 2 2
[1] FALSE
D42V8, continuous
[1] "Remove cluster labels:" "APC MUTATED"           
clus
  APC MUTATED APC WILD-TYPE 
            2            82 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8397    TCGA-62-8398 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P    TCGA-62-A46R 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y    TCGA-62-A470 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681    TCGA-64-5778 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520    TCGA-73-4662 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-73-4666    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498    TCGA-73-7499 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711    TCGA-86-7713 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055    TCGA-86-8056 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278    TCGA-86-8279 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668    TCGA-86-8669 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849    TCGA-93-7348 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458    TCGA-MN-A4N1 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-MN-A4N4    TCGA-MN-A4N5 
"APC WILD-TYPE" "APC WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  APC MUTATED                            0                                 9
  APC WILD-TYPE                         18                                93
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                   11
  APC WILD-TYPE                                                283
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  APC MUTATED                                            0
  APC WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  APC MUTATED                                               0
  APC WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  APC MUTATED                                0
  APC WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  APC MUTATED                                    0                            0
  APC WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  APC MUTATED                               0
  APC WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  APC MUTATED                                               0
  APC WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  APC MUTATED                              0
  APC WILD-TYPE                            9
D42V9, multiclass
                                                    clus
vv                                                   APC MUTATED APC WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            9            93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          11           283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
               cls
clus              0   1
  APC MUTATED     4  16
  APC WILD-TYPE  16 444
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      4   16
  APC WILD-TYPE   16  444
     clus
vv    APC MUTATED APC WILD-TYPE
  NO            4            16
  YES          16           444
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, continuous
               vv
clus             R0  R1  R2  RX
  APC MUTATED    13   0   1   0
  APC WILD-TYPE 297  11   3  25
D42V13, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          13           297
  R1           0            11
  R2           1             3
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APC MUTATED                                  0     0
  APC WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED                           1    15
  APC WILD-TYPE                        28   362
D42V14, multiclass
                                  clus
vv                                 APC MUTATED APC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     15           362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
               cls
clus              0   1
  APC MUTATED     0  14
  APC WILD-TYPE   6 335
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      0   14
  APC WILD-TYPE    6  335
                        clus
vv                       APC MUTATED APC WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          14           335
[1] 2 2
[1] FALSE

Clustering(43) Variable = STRA8 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  STRA8 MUTATED     6   2
  STRA8 WILD-TYPE 309 139
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             448 
  STRA8 MUTATED STRA8 WILD-TYPE 
              2             139 
$`STRA8 MUTATED`
TCGA-05-4382 TCGA-05-4397 TCGA-44-5643 TCGA-44-5644 TCGA-44-7670 TCGA-73-4668 
       19.96        24.03        33.30        28.37        29.00        15.35 
TCGA-78-7536 TCGA-86-8054 
        8.02        24.49 

$`STRA8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06         6.25        26.56        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       19.46        12.03         7.17        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        26.30         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        16.70         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  STRA8 MUTATED STRA8 WILD-TYPE 
           8.02            0.00 
  STRA8 MUTATED STRA8 WILD-TYPE 
          33.30          223.96 
  STRA8 MUTATED STRA8 WILD-TYPE 
         24.260          17.835 
[1] "8.0 - 33.3 (24.3)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D43V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STRA8 MUTATED         0        0        2         1         3          2
  STRA8 WILD-TYPE       4      123      131        45        64         68
                 vv
clus              STAGE IIIB STAGE IV
  STRA8 MUTATED            0        0
  STRA8 WILD-TYPE         11       25
D43V3, multiclass
            clus
vv           STRA8 MUTATED STRA8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               2             131
  STAGE IIA              1              45
  STAGE IIB              3              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STRA8 MUTATED     1   7   0   0
  STRA8 WILD-TYPE 154 254  43  18
D43V4, multiclass
    clus
vv   STRA8 MUTATED STRA8 WILD-TYPE
  T1             1             154
  T2             7             254
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  STRA8 MUTATED     2   4     2
  STRA8 WILD-TYPE 305  85    70
D43V5, multiclass
       clus
vv      STRA8 MUTATED STRA8 WILD-TYPE
  N0                2             305
  N1                4              85
  N2+N3             2              70
[1] 3 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
  STRA8 MUTATED     7   0
  STRA8 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      7    0
  STRA8 WILD-TYPE  320   23
   clus
vv  STRA8 MUTATED STRA8 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus                0   1
  STRA8 MUTATED     3   5
  STRA8 WILD-TYPE 256 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      3    5
  STRA8 WILD-TYPE  256  216
        clus
vv       STRA8 MUTATED STRA8 WILD-TYPE
  FEMALE             3             256
  MALE               5             216
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "STRA8 MUTATED"         
clus
  STRA8 MUTATED STRA8 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STRA8 MUTATED                            1                                 2
  STRA8 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STRA8 MUTATED                                                    4
  STRA8 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STRA8 MUTATED                                            0
  STRA8 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STRA8 MUTATED                                               0
  STRA8 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STRA8 MUTATED                                0
  STRA8 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STRA8 MUTATED                                    1
  STRA8 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STRA8 MUTATED                              0                             0
  STRA8 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STRA8 MUTATED                                               0
  STRA8 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STRA8 MUTATED                              0
  STRA8 WILD-TYPE                            9
D43V9, multiclass
                                                    clus
vv                                                   STRA8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STRA8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                 cls
clus                0   1
  STRA8 MUTATED     2   6
  STRA8 WILD-TYPE  18 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      2    6
  STRA8 WILD-TYPE   18  454
     clus
vv    STRA8 MUTATED STRA8 WILD-TYPE
  NO              2              18
  YES             6             454
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, continuous
                 vv
clus               R0  R1  R2  RX
  STRA8 MUTATED     5   0   0   0
  STRA8 WILD-TYPE 305  11   4  25
D43V13, multiclass
    clus
vv   STRA8 MUTATED STRA8 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STRA8 MUTATED                                  1     0
  STRA8 WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STRA8 MUTATED                           1     4
  STRA8 WILD-TYPE                        28   373
D43V14, multiclass
                                  clus
vv                                 STRA8 MUTATED STRA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                 cls
clus                0   1
  STRA8 MUTATED     1   4
  STRA8 WILD-TYPE   5 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      1    4
  STRA8 WILD-TYPE    5  345
                        clus
vv                       STRA8 MUTATED STRA8 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(44) Variable = A2M MUTATION ANALYSIS
D44V1, survival
               sevent
clus2             0   1
  A2M MUTATED    16   2
  A2M WILD-TYPE 299 139
  A2M MUTATED A2M WILD-TYPE 
           18           438 
  A2M MUTATED A2M WILD-TYPE 
            2           139 
$`A2M MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-38-4632 TCGA-55-1595 TCGA-55-8089 TCGA-55-8203 
        8.02        20.05        44.61        48.62         3.29        17.98 
TCGA-55-A490 TCGA-64-1676 TCGA-64-5781 TCGA-69-7980 TCGA-73-4670 TCGA-78-8640 
        1.58        56.81        51.25        12.56         4.31       214.62 
TCGA-86-8054 TCGA-91-6828 TCGA-91-6848 TCGA-95-7043 TCGA-97-7554 TCGA-MN-A4N4 
       24.49        10.62         7.36         1.22        25.48        38.63 

$`A2M WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
        0.00         9.96        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        11.64        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       23.05         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        2.93        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        10.55        32.68        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       13.87        20.55        19.43        19.89        16.70         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       17.62        13.64        26.47        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23        27.68         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  A2M MUTATED A2M WILD-TYPE 
         1.22          0.00 
  A2M MUTATED A2M WILD-TYPE 
       214.62        223.96 
  A2M MUTATED A2M WILD-TYPE 
       19.015        18.000 
[1] "1.2 - 214.6 (19.0)" "0.0 - 224.0 (18.0)"
[1] "hr=" "3.9"
D44V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  A2M MUTATED         1        6        4         2         2          2
  A2M WILD-TYPE       3      117      129        44        65         68
               vv
clus            STAGE IIIB STAGE IV
  A2M MUTATED            0        3
  A2M WILD-TYPE         11       22
D44V3, multiclass
            clus
vv           A2M MUTATED A2M WILD-TYPE
  STAGE I              1             3
  STAGE IA             6           117
  STAGE IB             4           129
  STAGE IIA            2            44
  STAGE IIB            2            65
  STAGE IIIA           2            68
  STAGE IIIB           0            11
  STAGE IV             3            22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  A2M MUTATED     9  10   1   0
  A2M WILD-TYPE 146 251  42  18
D44V4, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  T1           9           146
  T2          10           251
  T3           1            42
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  A2M MUTATED    14   3     2
  A2M WILD-TYPE 293  86    70
D44V5, multiclass
       clus
vv      A2M MUTATED A2M WILD-TYPE
  N0             14           293
  N1              3            86
  N2+N3           2            70
[1] 3 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
  A2M MUTATED    13   3
  A2M WILD-TYPE 314  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     13    3
  A2M WILD-TYPE  314   20
   clus
vv  A2M MUTATED A2M WILD-TYPE
  0          13           314
  1           3            20
[1] 2 2
[1] FALSE
D44V7, binary
               cls
clus              0   1
  A2M MUTATED    10  10
  A2M WILD-TYPE 249 211
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     10   10
  A2M WILD-TYPE  249  211
        clus
vv       A2M MUTATED A2M WILD-TYPE
  FEMALE          10           249
  MALE            10           211
[1] 2 2
[1] FALSE
D44V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  A2M MUTATED                            1                                 4
  A2M WILD-TYPE                         17                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  A2M MUTATED                                                   13
  A2M WILD-TYPE                                                281
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  A2M MUTATED                                            0
  A2M WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  A2M MUTATED                                               0
  A2M WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  A2M MUTATED                                1
  A2M WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  A2M MUTATED                                    0                            0
  A2M WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  A2M MUTATED                               1
  A2M WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  A2M MUTATED                                               0
  A2M WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  A2M MUTATED                              0
  A2M WILD-TYPE                            9
D44V9, multiclass
                                                    clus
vv                                                   A2M MUTATED A2M WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          13           281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
               cls
clus              0   1
  A2M MUTATED     0  20
  A2M WILD-TYPE  20 440
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED      0   20
  A2M WILD-TYPE   20  440
     clus
vv    A2M MUTATED A2M WILD-TYPE
  NO            0            20
  YES          20           440
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, continuous
               vv
clus             R0  R1  R2  RX
  A2M MUTATED    15   0   1   0
  A2M WILD-TYPE 295  11   3  25
D44V13, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  R0          15           295
  R1           0            11
  R2           1             3
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  A2M MUTATED                                  0     1
  A2M WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  A2M MUTATED                           1    13
  A2M WILD-TYPE                        28   364
D44V14, multiclass
                                  clus
vv                                 A2M MUTATED A2M WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     13           364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
               cls
clus              0   1
  A2M MUTATED     0  15
  A2M WILD-TYPE   6 334
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED      0   15
  A2M WILD-TYPE    6  334
                        clus
vv                       A2M MUTATED A2M WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          15           334
[1] 2 2
[1] FALSE

Clustering(45) Variable = CD244 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2               0   1
  CD244 MUTATED     7   4
  CD244 WILD-TYPE 308 137
  CD244 MUTATED CD244 WILD-TYPE 
             11             445 
  CD244 MUTATED CD244 WILD-TYPE 
              4             137 
$`CD244 MUTATED`
TCGA-44-2656 TCGA-44-7670 TCGA-44-7672 TCGA-50-5045 TCGA-55-8092 TCGA-55-8096 
       46.98        29.00        23.64        71.47         5.06        23.64 
TCGA-55-8506 TCGA-69-7979 TCGA-78-7220 TCGA-86-8358 TCGA-97-A4M5 
        0.36         2.93        26.53        21.47        20.84 

$`CD244 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       36.07        18.87        17.59        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
      104.19       223.96         8.48        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       19.76        20.52        17.75        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CD244 MUTATED CD244 WILD-TYPE 
           0.36            0.00 
  CD244 MUTATED CD244 WILD-TYPE 
          71.47          223.96 
  CD244 MUTATED CD244 WILD-TYPE 
          23.64           17.75 
[1] "0.4 - 71.5 (23.6)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D45V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CD244 MUTATED         0        3        5         1         2          1
  CD244 WILD-TYPE       4      120      128        45        65         69
                 vv
clus              STAGE IIIB STAGE IV
  CD244 MUTATED            0        0
  CD244 WILD-TYPE         11       25
D45V3, multiclass
            clus
vv           CD244 MUTATED CD244 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               5             128
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD244 MUTATED     3   7   2   0
  CD244 WILD-TYPE 152 254  41  18
D45V4, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  T1             3             152
  T2             7             254
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  CD244 MUTATED     9   2     1
  CD244 WILD-TYPE 298  87    71
D45V5, multiclass
       clus
vv      CD244 MUTATED CD244 WILD-TYPE
  N0                9             298
  N1                2              87
  N2+N3             1              71
[1] 3 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
  CD244 MUTATED     8   0
  CD244 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      8    0
  CD244 WILD-TYPE  319   23
   clus
vv  CD244 MUTATED CD244 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D45V7, binary
                 cls
clus                0   1
  CD244 MUTATED     8   4
  CD244 WILD-TYPE 251 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      8    4
  CD244 WILD-TYPE  251  217
        clus
vv       CD244 MUTATED CD244 WILD-TYPE
  FEMALE             8             251
  MALE               4             217
[1] 2 2
[1] FALSE
D45V8, continuous
[1] "Remove cluster labels:" "CD244 MUTATED"         
clus
  CD244 MUTATED CD244 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8205      TCGA-55-8208 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8359 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CD244 MUTATED                            1                                 2
  CD244 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CD244 MUTATED                                                    9
  CD244 WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CD244 MUTATED                                            0
  CD244 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CD244 MUTATED                                               0
  CD244 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CD244 MUTATED                                0
  CD244 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CD244 MUTATED                                    0
  CD244 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CD244 MUTATED                              0                             0
  CD244 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CD244 MUTATED                                               0
  CD244 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CD244 MUTATED                              0
  CD244 WILD-TYPE                            9
D45V9, multiclass
                                                    clus
vv                                                   CD244 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CD244 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                 cls
clus                0   1
  CD244 MUTATED     2  10
  CD244 WILD-TYPE  18 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      2   10
  CD244 WILD-TYPE   18  450
     clus
vv    CD244 MUTATED CD244 WILD-TYPE
  NO              2              18
  YES            10             450
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, continuous
                 vv
clus               R0  R1  R2  RX
  CD244 MUTATED     5   0   0   0
  CD244 WILD-TYPE 305  11   4  25
D45V13, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD244 MUTATED                                  0     0
  CD244 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD244 MUTATED                           1    10
  CD244 WILD-TYPE                        28   367
D45V14, multiclass
                                  clus
vv                                 CD244 MUTATED CD244 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                 cls
clus                0   1
  CD244 MUTATED     1   9
  CD244 WILD-TYPE   5 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      1    9
  CD244 WILD-TYPE    5  340
                        clus
vv                       CD244 MUTATED CD244 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(46) Variable = SRPX MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  SRPX MUTATED    11   5
  SRPX WILD-TYPE 304 136
  SRPX MUTATED SRPX WILD-TYPE 
            16            440 
  SRPX MUTATED SRPX WILD-TYPE 
             5            136 
$`SRPX MUTATED`
TCGA-05-4390 TCGA-05-4432 TCGA-38-4628 TCGA-44-2665 TCGA-44-3396 TCGA-44-7659 
       37.02        25.02        49.05        42.77        37.15        14.60 
TCGA-49-4514 TCGA-50-6593 TCGA-50-6594 TCGA-55-8094 TCGA-78-7155 TCGA-93-7348 
       55.89        11.05        12.16         0.13        38.50         4.18 
TCGA-95-7043 TCGA-97-7938 TCGA-97-A4LX TCGA-97-A4M6 
        1.22         0.59        20.19        18.67 

$`SRPX WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-3398 TCGA-44-3918 
        4.37        46.98        13.15        24.36        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 
       63.72        32.45        61.28        16.44        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       25.55         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN 
        1.18         1.45        19.82         9.76         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.12         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       25.48         5.95         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 
       21.44        19.76        20.52        17.75        20.84        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SRPX MUTATED SRPX WILD-TYPE 
          0.13           0.00 
  SRPX MUTATED SRPX WILD-TYPE 
         55.89         223.96 
  SRPX MUTATED SRPX WILD-TYPE 
         19.43          17.95 
[1] "0.1 - 55.9 (19.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1"  
D46V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SRPX MUTATED         0        6        3         0         3          3
  SRPX WILD-TYPE       4      117      130        46        64         67
                vv
clus             STAGE IIIB STAGE IV
  SRPX MUTATED            0        1
  SRPX WILD-TYPE         11       24
D46V3, multiclass
            clus
vv           SRPX MUTATED SRPX WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            3             67
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SRPX MUTATED     7   8   1   0
  SRPX WILD-TYPE 148 253  42  18
D46V4, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  T1            7            148
  T2            8            253
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  SRPX MUTATED    10   3     3
  SRPX WILD-TYPE 297  86    69
D46V5, multiclass
       clus
vv      SRPX MUTATED SRPX WILD-TYPE
  N0              10            297
  N1               3             86
  N2+N3            3             69
[1] 3 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
  SRPX MUTATED    11   1
  SRPX WILD-TYPE 316  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED     11    1
  SRPX WILD-TYPE  316   22
   clus
vv  SRPX MUTATED SRPX WILD-TYPE
  0           11            316
  1            1             22
[1] 2 2
[1] FALSE
D46V7, binary
                cls
clus               0   1
  SRPX MUTATED    11   5
  SRPX WILD-TYPE 248 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED     11    5
  SRPX WILD-TYPE  248  216
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE           11            248
  MALE              5            216
[1] 2 2
[1] FALSE
D46V8, continuous
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7711 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7954     TCGA-86-7955 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8074     TCGA-86-8075 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8281 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SRPX MUTATED                            0                                 6
  SRPX WILD-TYPE                         18                                96
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SRPX MUTATED                                                    8
  SRPX WILD-TYPE                                                286
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SRPX MUTATED                                            0
  SRPX WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SRPX MUTATED                                               1
  SRPX WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SRPX MUTATED                                0
  SRPX WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SRPX MUTATED                                    0
  SRPX WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SRPX MUTATED                              0                             1
  SRPX WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SRPX MUTATED                                               0
  SRPX WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SRPX MUTATED                              0
  SRPX WILD-TYPE                            9
D46V9, multiclass
                                                    clus
vv                                                   SRPX MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SRPX WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                cls
clus               0   1
  SRPX MUTATED     0  16
  SRPX WILD-TYPE  20 444
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      0   16
  SRPX WILD-TYPE   20  444
     clus
vv    SRPX MUTATED SRPX WILD-TYPE
  NO             0             20
  YES           16            444
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, continuous
                vv
clus              R0  R1  R2  RX
  SRPX MUTATED    11   0   0   0
  SRPX WILD-TYPE 299  11   4  25
D46V13, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  R0           11            299
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRPX MUTATED                                  0     0
  SRPX WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SRPX MUTATED                           1    13
  SRPX WILD-TYPE                        28   364
D46V14, multiclass
                                  clus
vv                                 SRPX MUTATED SRPX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      13            364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                cls
clus               0   1
  SRPX MUTATED     0  12
  SRPX WILD-TYPE   6 337
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      0   12
  SRPX WILD-TYPE    6  337
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           12            337
[1] 2 2
[1] FALSE

Clustering(47) Variable = GAGE2D MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2                0   1
  GAGE2D MUTATED     3   2
  GAGE2D WILD-TYPE 312 139
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               5              451 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               2              139 
$`GAGE2D MUTATED`
TCGA-44-3396 TCGA-44-6779 TCGA-55-1592 TCGA-55-8302 TCGA-86-8674 
       37.15        16.44        23.05         0.76        13.32 

$`GAGE2D WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  GAGE2D MUTATED GAGE2D WILD-TYPE 
            0.76             0.00 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
           37.15           223.96 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
           16.44            18.08 
[1] "0.8 - 37.1 (16.4)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.9"
D47V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GAGE2D MUTATED         0        1        1         1         1          1
  GAGE2D WILD-TYPE       4      122      132        45        66         69
                  vv
clus               STAGE IIIB STAGE IV
  GAGE2D MUTATED            0        0
  GAGE2D WILD-TYPE         11       25
D47V3, multiclass
            clus
vv           GAGE2D MUTATED GAGE2D WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                1              132
  STAGE IIA               1               45
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GAGE2D MUTATED     0   5   0   0
  GAGE2D WILD-TYPE 155 256  43  18
D47V4, multiclass
    clus
vv   GAGE2D MUTATED GAGE2D WILD-TYPE
  T1              0              155
  T2              5              256
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  GAGE2D MUTATED     2   2     1
  GAGE2D WILD-TYPE 305  87    71
D47V5, multiclass
       clus
vv      GAGE2D MUTATED GAGE2D WILD-TYPE
  N0                 2              305
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  GAGE2D MUTATED     3   0
  GAGE2D WILD-TYPE 324  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      3    0
  GAGE2D WILD-TYPE  324   23
   clus
vv  GAGE2D MUTATED GAGE2D WILD-TYPE
  0              3              324
  1              0               23
[1] 2 2
[1] FALSE
D47V7, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     2   3
  GAGE2D WILD-TYPE 257 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      2    3
  GAGE2D WILD-TYPE  257  218
        clus
vv       GAGE2D MUTATED GAGE2D WILD-TYPE
  FEMALE              2              257
  MALE                3              218
[1] 2 2
[1] FALSE
D47V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GAGE2D MUTATED                            0                                 0
  GAGE2D WILD-TYPE                         18                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GAGE2D MUTATED                                                    4
  GAGE2D WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GAGE2D MUTATED                                            0
  GAGE2D WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GAGE2D MUTATED                                               0
  GAGE2D WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  GAGE2D MUTATED                                0
  GAGE2D WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  GAGE2D MUTATED                                    0
  GAGE2D WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GAGE2D MUTATED                              0                             1
  GAGE2D WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GAGE2D MUTATED                                               0
  GAGE2D WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  GAGE2D MUTATED                              0
  GAGE2D WILD-TYPE                            9
D47V9, multiclass
                                                    clus
vv                                                   GAGE2D MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   GAGE2D WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     0   5
  GAGE2D WILD-TYPE  20 455
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      0    5
  GAGE2D WILD-TYPE   20  455
     clus
vv    GAGE2D MUTATED GAGE2D WILD-TYPE
  NO               0               20
  YES              5              455
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, continuous
                  vv
clus                R0  R1  R2  RX
  GAGE2D MUTATED     4   0   0   0
  GAGE2D WILD-TYPE 306  11   4  25
D47V13, multiclass
    clus
vv   GAGE2D MUTATED GAGE2D WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAGE2D MUTATED                                  0     0
  GAGE2D WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAGE2D MUTATED                           0     5
  GAGE2D WILD-TYPE                        29   372
D47V14, multiclass
                                  clus
vv                                 GAGE2D MUTATED GAGE2D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     0   3
  GAGE2D WILD-TYPE   6 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      0    3
  GAGE2D WILD-TYPE    6  346
                        clus
vv                       GAGE2D MUTATED GAGE2D WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              3              346
[1] 2 2
[1] FALSE

Clustering(48) Variable = ADNP2 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  ADNP2 MUTATED    14   9
  ADNP2 WILD-TYPE 301 132
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             23             433 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              9             132 
$`ADNP2 MUTATED`
TCGA-05-4250 TCGA-50-5049 TCGA-50-6590 TCGA-55-6979 TCGA-55-7728 TCGA-55-7815 
        3.98        70.55        42.35         7.79         0.79         1.78 
TCGA-55-8092 TCGA-55-8208 TCGA-55-8506 TCGA-55-A491 TCGA-62-8394 TCGA-62-A46O 
        5.06        22.16         0.36        20.58         4.57        47.80 
TCGA-67-3771 TCGA-73-4668 TCGA-78-7147 TCGA-78-7158 TCGA-86-8358 TCGA-86-8674 
       20.05        15.35        19.27         5.88        21.47        13.32 
TCGA-86-A4JF TCGA-93-7348 TCGA-99-7458 TCGA-MN-A4N1 TCGA-MP-A4TK 
       17.62         4.18        24.56        27.19        19.13 

$`ADNP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       17.16        11.64        22.26        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        22.55         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         1.28         1.12         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.66        19.73         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40         1.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       19.99        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       28.47        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       29.98        26.30         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
       39.09        23.51       163.10        27.16         5.69        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       32.09        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82         9.76         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        20.68        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81         0.20        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        14.10        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ADNP2 MUTATED ADNP2 WILD-TYPE 
           0.36            0.00 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
          70.55          223.96 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
          17.62           18.08 
[1] "0.4 - 70.5 (17.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.8"
D48V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADNP2 MUTATED         0        5        6         2         7          2
  ADNP2 WILD-TYPE       4      118      127        44        60         68
                 vv
clus              STAGE IIIB STAGE IV
  ADNP2 MUTATED            2        0
  ADNP2 WILD-TYPE          9       25
D48V3, multiclass
            clus
vv           ADNP2 MUTATED ADNP2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               6             127
  STAGE IIA              2              44
  STAGE IIB              7              60
  STAGE IIIA             2              68
  STAGE IIIB             2               9
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of 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     4  13   4   3
  ADNP2 WILD-TYPE 151 248  39  15
D48V4, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  T1             4             151
  T2            13             248
  T3             4              39
  T4             3              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"
                 vv
clus               N0  N1 N2+N3
  ADNP2 MUTATED    15   7     2
  ADNP2 WILD-TYPE 292  82    70
D48V5, multiclass
       clus
vv      ADNP2 MUTATED ADNP2 WILD-TYPE
  N0               15             292
  N1                7              82
  N2+N3             2              70
[1] 3 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
  ADNP2 MUTATED    17   0
  ADNP2 WILD-TYPE 310  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     17    0
  ADNP2 WILD-TYPE  310   23
   clus
vv  ADNP2 MUTATED ADNP2 WILD-TYPE
  0            17             310
  1             0              23
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus                0   1
  ADNP2 MUTATED    16   8
  ADNP2 WILD-TYPE 243 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     16    8
  ADNP2 WILD-TYPE  243  213
        clus
vv       ADNP2 MUTATED ADNP2 WILD-TYPE
  FEMALE            16             243
  MALE               8             213
[1] 2 2
[1] FALSE
D48V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADNP2 MUTATED                            0                                 3
  ADNP2 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADNP2 MUTATED                                                   17
  ADNP2 WILD-TYPE                                                277
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADNP2 MUTATED                                            0
  ADNP2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADNP2 MUTATED                                               1
  ADNP2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ADNP2 MUTATED                                0
  ADNP2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ADNP2 MUTATED                                    1
  ADNP2 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADNP2 MUTATED                              0                             1
  ADNP2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADNP2 MUTATED                                               0
  ADNP2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ADNP2 MUTATED                              1
  ADNP2 WILD-TYPE                            8
D48V9, multiclass
                                                    clus
vv                                                   ADNP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   ADNP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                 cls
clus                0   1
  ADNP2 MUTATED     1  23
  ADNP2 WILD-TYPE  19 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      1   23
  ADNP2 WILD-TYPE   19  437
     clus
vv    ADNP2 MUTATED ADNP2 WILD-TYPE
  NO              1              19
  YES            23             437
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, continuous
                 vv
clus               R0  R1  R2  RX
  ADNP2 MUTATED    18   1   1   1
  ADNP2 WILD-TYPE 292  10   3  24
D48V13, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  R0            18             292
  R1             1              10
  R2             1               3
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADNP2 MUTATED                                  1     0
  ADNP2 WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADNP2 MUTATED                           2    16
  ADNP2 WILD-TYPE                        27   361
D48V14, multiclass
                                  clus
vv                                 ADNP2 MUTATED ADNP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       16             361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                 cls
clus                0   1
  ADNP2 MUTATED     0  16
  ADNP2 WILD-TYPE   6 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      0   16
  ADNP2 WILD-TYPE    6  333
                        clus
vv                       ADNP2 MUTATED ADNP2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            16             333
[1] 2 2
[1] FALSE

Clustering(49) Variable = GLDC MUTATION ANALYSIS
D49V1, survival
                sevent
clus2              0   1
  GLDC MUTATED    15   6
  GLDC WILD-TYPE 300 135
  GLDC MUTATED GLDC WILD-TYPE 
            21            435 
  GLDC MUTATED GLDC WILD-TYPE 
             6            135 
$`GLDC MUTATED`
TCGA-05-4417 TCGA-05-4427 TCGA-38-4629 TCGA-38-7271 TCGA-44-2656 TCGA-44-3918 
       14.96        26.01        28.41        26.30        46.98        34.06 
TCGA-44-5644 TCGA-53-7624 TCGA-55-5899 TCGA-55-7911 TCGA-55-7994 TCGA-55-8508 
       28.37        34.29         2.86        17.65        19.82         0.49 
TCGA-78-7150 TCGA-78-7156 TCGA-78-7542 TCGA-91-6848 TCGA-95-7043 TCGA-95-7944 
       21.90        32.09        10.55         7.36         1.22        12.39 
TCGA-95-A4VN TCGA-L4-A4E5 TCGA-MN-A4N4 
       18.18        19.00        38.63 

$`GLDC WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F 
       49.05        35.28        11.64        44.61        14.73         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
       13.15        24.36        42.77        37.15        38.24         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05        48.62         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 
        1.45        18.64         0.53         6.48         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58        35.93        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 
        8.02        53.33        10.75        39.35        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       16.44        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  GLDC MUTATED GLDC WILD-TYPE 
          0.49           0.00 
  GLDC MUTATED GLDC WILD-TYPE 
         46.98         223.96 
  GLDC MUTATED GLDC WILD-TYPE 
         19.82          17.75 
[1] "0.5 - 47.0 (19.8)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D49V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GLDC MUTATED         1        7        4         2         4          1
  GLDC WILD-TYPE       3      116      129        44        63         69
                vv
clus             STAGE IIIB STAGE IV
  GLDC MUTATED            0        2
  GLDC WILD-TYPE         11       23
D49V3, multiclass
            clus
vv           GLDC MUTATED GLDC WILD-TYPE
  STAGE I               1              3
  STAGE IA              7            116
  STAGE IB              4            129
  STAGE IIA             2             44
  STAGE IIB             4             63
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLDC MUTATED     8  10   2   1
  GLDC WILD-TYPE 147 251  41  17
D49V4, multiclass
    clus
vv   GLDC MUTATED GLDC WILD-TYPE
  T1            8            147
  T2           10            251
  T3            2             41
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  GLDC MUTATED    14   6     1
  GLDC WILD-TYPE 293  83    71
D49V5, multiclass
       clus
vv      GLDC MUTATED GLDC WILD-TYPE
  N0              14            293
  N1               6             83
  N2+N3            1             71
[1] 3 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
  GLDC MUTATED    13   2
  GLDC WILD-TYPE 314  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDC MUTATED     13    2
  GLDC WILD-TYPE  314   21
   clus
vv  GLDC MUTATED GLDC WILD-TYPE
  0           13            314
  1            2             21
[1] 2 2
[1] FALSE
D49V7, binary
                cls
clus               0   1
  GLDC MUTATED    11  10
  GLDC WILD-TYPE 248 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDC MUTATED     11   10
  GLDC WILD-TYPE  248  211
        clus
vv       GLDC MUTATED GLDC WILD-TYPE
  FEMALE           11            248
  MALE             10            211
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "GLDC MUTATED"          
clus
  GLDC MUTATED GLDC WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" "GLDC WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N5 
"GLDC WILD-TYPE" "GLDC WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GLDC MUTATED                            0                                 4
  GLDC WILD-TYPE                         18                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GLDC MUTATED                                                   15
  GLDC WILD-TYPE                                                279
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GLDC MUTATED                                            0
  GLDC WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GLDC MUTATED                                               0
  GLDC WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  GLDC MUTATED                                0
  GLDC WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  GLDC MUTATED                                    0
  GLDC WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GLDC MUTATED                              0                             0
  GLDC WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GLDC MUTATED                                               1
  GLDC WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  GLDC MUTATED                              1
  GLDC WILD-TYPE                            8
D49V9, multiclass
                                                    clus
vv                                                   GLDC MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   GLDC WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                cls
clus               0   1
  GLDC MUTATED     0  21
  GLDC WILD-TYPE  20 439
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDC MUTATED      0   21
  GLDC WILD-TYPE   20  439
     clus
vv    GLDC MUTATED GLDC WILD-TYPE
  NO             0             20
  YES           21            439
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, continuous
                vv
clus              R0  R1  R2  RX
  GLDC MUTATED    17   0   0   0
  GLDC WILD-TYPE 293  11   4  25
D49V13, multiclass
    clus
vv   GLDC MUTATED GLDC WILD-TYPE
  R0           17            293
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLDC MUTATED                                  0     0
  GLDC WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLDC MUTATED                           1    18
  GLDC WILD-TYPE                        28   359
D49V14, multiclass
                                  clus
vv                                 GLDC MUTATED GLDC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      18            359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                cls
clus               0   1
  GLDC MUTATED     1  15
  GLDC WILD-TYPE   5 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDC MUTATED      1   15
  GLDC WILD-TYPE    5  334
                        clus
vv                       GLDC MUTATED GLDC WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           15            334
[1] 2 2
[1] FALSE

Clustering(50) Variable = PIK3CA MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    15  11
  PIK3CA WILD-TYPE 300 130
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              430 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              11              130 
$`PIK3CA MUTATED`
TCGA-05-4249 TCGA-05-4397 TCGA-44-5643 TCGA-44-5645 TCGA-44-7670 TCGA-49-6743 
       50.07        24.03        33.30        12.59        29.00        12.13 
TCGA-50-5044 TCGA-50-6590 TCGA-50-6592 TCGA-55-7574 TCGA-55-7724 TCGA-55-7995 
       20.52        42.35        25.55         3.12        23.18         0.16 
TCGA-55-8092 TCGA-64-1677 TCGA-73-7499 TCGA-78-7146 TCGA-78-7153 TCGA-86-7714 
        5.06        20.65        23.51         5.69        24.99        20.55 
TCGA-93-7348 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-97-8177 TCGA-97-8552 
        4.18         2.86        15.68        15.65        16.41        20.58 
TCGA-MP-A4SY TCGA-MP-A4TI 
       49.35        14.10 

$`PIK3CA WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       37.15        38.24        34.06         6.25        26.56        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       19.46        12.03         7.17        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 
       29.26        17.16        11.64        22.26        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 
       18.64        29.03        25.12        22.55         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
        1.15         7.99         0.20         0.13         1.32         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
        0.53         6.48        17.65         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.66        19.73         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       39.09       163.10        27.16        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        13.87        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         1.22        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
       27.19        38.63         2.76        86.14        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        2.43        10.09        29.46        11.05        14.66        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.16             0.00 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           50.07           223.96 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          20.535           17.950 
[1] "0.2 - 50.1 (20.5)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.7"
D50V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PIK3CA MUTATED         1        4        9         3         4          6
  PIK3CA WILD-TYPE       3      119      124        43        63         64
                  vv
clus               STAGE IIIB STAGE IV
  PIK3CA MUTATED            1        0
  PIK3CA WILD-TYPE         10       25
D50V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 1                3
  STAGE IA                4              119
  STAGE IB                9              124
  STAGE IIA               3               43
  STAGE IIB               4               63
  STAGE IIIA              6               64
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     8  18   1   1
  PIK3CA WILD-TYPE 147 243  42  17
D50V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              8              147
  T2             18              243
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  PIK3CA MUTATED    14   7     6
  PIK3CA WILD-TYPE 293  82    66
D50V5, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  N0                14              293
  N1                 7               82
  N2+N3              6               66
[1] 3 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
  PIK3CA MUTATED    22   0
  PIK3CA WILD-TYPE 305  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     22    0
  PIK3CA WILD-TYPE  305   23
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             22              305
  1              0               23
[1] 2 2
[1] FALSE
D50V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    20   8
  PIK3CA WILD-TYPE 239 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     20    8
  PIK3CA WILD-TYPE  239  213
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             20              239
  MALE                8              213
[1] 2 2
[1] FALSE
D50V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PIK3CA MUTATED                            0                                 8
  PIK3CA WILD-TYPE                         18                                94
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                   18
  PIK3CA WILD-TYPE                                                276
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PIK3CA MUTATED                                            0
  PIK3CA WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PIK3CA MUTATED                                               1
  PIK3CA WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  PIK3CA MUTATED                                1
  PIK3CA WILD-TYPE                              1
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  PIK3CA MUTATED                                    0
  PIK3CA WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PIK3CA MUTATED                              0                             0
  PIK3CA WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PIK3CA MUTATED                                               0
  PIK3CA WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  PIK3CA MUTATED                              0
  PIK3CA WILD-TYPE                            9
D50V9, multiclass
                                                    clus
vv                                                   PIK3CA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             18
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   PIK3CA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     2  26
  PIK3CA WILD-TYPE  18 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      2   26
  PIK3CA WILD-TYPE   18  434
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               2               18
  YES             26              434
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, continuous
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    17   1   0   1
  PIK3CA WILD-TYPE 293  10   4  24
D50V13, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             17              293
  R1              1               10
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     0
  PIK3CA WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           4    20
  PIK3CA WILD-TYPE                        25   357
D50V14, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     4               25
  WHITE                                        20              357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  20
  PIK3CA WILD-TYPE   5 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   20
  PIK3CA WILD-TYPE    5  329
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             20              329
[1] 2 2
[1] FALSE

Clustering(51) Variable = MED12 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  MED12 MUTATED    21  15
  MED12 WILD-TYPE 294 126
  MED12 MUTATED MED12 WILD-TYPE 
             36             420 
  MED12 MUTATED MED12 WILD-TYPE 
             15             126 
$`MED12 MUTATED`
TCGA-05-4390 TCGA-05-4397 TCGA-05-4430 TCGA-44-6777 TCGA-44-6779 TCGA-44-A47A 
       37.02        24.03        25.02        32.45        16.44        15.32 
TCGA-49-4488 TCGA-49-4507 TCGA-50-5051 TCGA-50-6594 TCGA-55-6968 TCGA-55-7281 
       28.57         8.81        15.72        12.16        42.51         0.59 
TCGA-55-7907 TCGA-55-7995 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8514 
        0.53         0.16         1.08        22.16        15.42         6.64 
TCGA-55-A492 TCGA-55-A494 TCGA-62-A46O TCGA-69-7979 TCGA-69-7980 TCGA-78-7154 
       19.59        15.81        47.80         2.93        12.56        19.50 
TCGA-78-7156 TCGA-78-7220 TCGA-83-5908 TCGA-86-7954 TCGA-91-6830 TCGA-95-7043 
       32.09        26.53        27.09        19.89         1.97         1.22 
TCGA-95-7947 TCGA-99-7458 TCGA-J2-8194 TCGA-MP-A4T4 TCGA-MP-A4TF TCGA-MP-A5C7 
       15.68        24.56        23.80        86.04        11.05        73.91 

$`MED12 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        63.72        61.28        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       23.64        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       12.66        35.54        46.72        14.07        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
       11.64        22.26        20.52        71.47        70.55        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       48.62         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         1.74         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 
        1.12         0.79         1.78         1.45        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       17.98         1.51         2.17         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       39.52        24.99        38.50         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
        7.07       104.19       223.96         8.48        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 
      214.62        39.75        77.59        10.55       110.50        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.12         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       18.67        12.39        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        19.13        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MED12 MUTATED MED12 WILD-TYPE 
           0.16            0.00 
  MED12 MUTATED MED12 WILD-TYPE 
          86.04          223.96 
  MED12 MUTATED MED12 WILD-TYPE 
          17.97           18.03 
[1] "0.2 - 86.0 (18.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D51V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MED12 MUTATED         1        9       10         3         5          7
  MED12 WILD-TYPE       3      114      123        43        62         63
                 vv
clus              STAGE IIIB STAGE IV
  MED12 MUTATED            0        2
  MED12 WILD-TYPE         11       23
D51V3, multiclass
            clus
vv           MED12 MUTATED MED12 WILD-TYPE
  STAGE I                1               3
  STAGE IA               9             114
  STAGE IB              10             123
  STAGE IIA              3              43
  STAGE IIB              5              62
  STAGE IIIA             7              63
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MED12 MUTATED    12  19   4   2
  MED12 WILD-TYPE 143 242  39  16
D51V4, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  T1            12             143
  T2            19             242
  T3             4              39
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  MED12 MUTATED    24   7     5
  MED12 WILD-TYPE 283  82    67
D51V5, multiclass
       clus
vv      MED12 MUTATED MED12 WILD-TYPE
  N0               24             283
  N1                7              82
  N2+N3             5              67
[1] 3 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
  MED12 MUTATED    22   2
  MED12 WILD-TYPE 305  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED     22    2
  MED12 WILD-TYPE  305   21
   clus
vv  MED12 MUTATED MED12 WILD-TYPE
  0            22             305
  1             2              21
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus                0   1
  MED12 MUTATED    31   6
  MED12 WILD-TYPE 228 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED     31    6
  MED12 WILD-TYPE  228  215
        clus
vv       MED12 MUTATED MED12 WILD-TYPE
  FEMALE            31             228
  MALE               6             215
[1] 2 2
[1] FALSE
D51V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MED12 MUTATED                            1                                 8
  MED12 WILD-TYPE                         17                                94
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MED12 MUTATED                                                   26
  MED12 WILD-TYPE                                                268
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MED12 MUTATED                                            0
  MED12 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MED12 MUTATED                                               2
  MED12 WILD-TYPE                                            17
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MED12 MUTATED                                0
  MED12 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MED12 MUTATED                                    0
  MED12 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MED12 MUTATED                              0                             0
  MED12 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MED12 MUTATED                                               0
  MED12 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MED12 MUTATED                              0
  MED12 WILD-TYPE                            9
D51V9, multiclass
                                                    clus
vv                                                   MED12 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            26
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  2
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MED12 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             268
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   17
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                 cls
clus                0   1
  MED12 MUTATED     4  33
  MED12 WILD-TYPE  16 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      4   33
  MED12 WILD-TYPE   16  427
     clus
vv    MED12 MUTATED MED12 WILD-TYPE
  NO              4              16
  YES            33             427
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, continuous
                 vv
clus               R0  R1  R2  RX
  MED12 MUTATED    28   0   0   0
  MED12 WILD-TYPE 282  11   4  25
D51V13, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  R0            28             282
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED12 MUTATED                                  0     0
  MED12 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED12 MUTATED                           2    31
  MED12 WILD-TYPE                        27   346
D51V14, multiclass
                                  clus
vv                                 MED12 MUTATED MED12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       31             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                 cls
clus                0   1
  MED12 MUTATED     0  26
  MED12 WILD-TYPE   6 323
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      0   26
  MED12 WILD-TYPE    6  323
                        clus
vv                       MED12 MUTATED MED12 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            26             323
[1] 2 2
[1] FALSE

Clustering(52) Variable = TRERF1 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED     8   9
  TRERF1 WILD-TYPE 307 132
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              17              439 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               9              132 
$`TRERF1 MUTATED`
TCGA-05-4250 TCGA-05-5420 TCGA-44-7670 TCGA-49-4488 TCGA-55-7907 TCGA-55-8511 
        3.98        15.02        29.00        28.57         0.53         0.30 
TCGA-62-A46O TCGA-64-1677 TCGA-69-7978 TCGA-78-7145 TCGA-78-7155 TCGA-78-7220 
       47.80        20.65         2.30        27.16        38.50        26.53 
TCGA-78-8662 TCGA-93-8067 TCGA-95-8494 TCGA-J2-8194 TCGA-O1-A52J 
      110.50         6.12         2.76        23.80        59.11 

$`TRERF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.11        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       23.51       163.10         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82         9.76         4.18        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.68        15.65        27.29        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R 
       19.82 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
             0.3              0.0 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          110.50           223.96 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           23.80            17.92 
[1] "0.3 - 110.5 (23.8)" "0.0 - 224.0 (17.9)"
[1] "hr=" "1.4"
D52V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TRERF1 MUTATED         0        2        6         3         2          4
  TRERF1 WILD-TYPE       4      121      127        43        65         66
                  vv
clus               STAGE IIIB STAGE IV
  TRERF1 MUTATED            0        1
  TRERF1 WILD-TYPE         11       24
D52V3, multiclass
            clus
vv           TRERF1 MUTATED TRERF1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                6              127
  STAGE IIA               3               43
  STAGE IIB               2               65
  STAGE IIIA              4               66
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRERF1 MUTATED     3  12   2   1
  TRERF1 WILD-TYPE 152 249  41  17
D52V4, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  T1              3              152
  T2             12              249
  T3              2               41
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  TRERF1 MUTATED     9   6     3
  TRERF1 WILD-TYPE 298  83    69
D52V5, multiclass
       clus
vv      TRERF1 MUTATED TRERF1 WILD-TYPE
  N0                 9              298
  N1                 6               83
  N2+N3              3               69
[1] 3 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
  TRERF1 MUTATED     9   1
  TRERF1 WILD-TYPE 318  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      9    1
  TRERF1 WILD-TYPE  318   22
   clus
vv  TRERF1 MUTATED TRERF1 WILD-TYPE
  0              9              318
  1              1               22
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    12   6
  TRERF1 WILD-TYPE 247 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     12    6
  TRERF1 WILD-TYPE  247  215
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE             12              247
  MALE                6              215
[1] 2 2
[1] FALSE
D52V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TRERF1 MUTATED                            0                                 3
  TRERF1 WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TRERF1 MUTATED                                                   15
  TRERF1 WILD-TYPE                                                279
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TRERF1 MUTATED                                            0
  TRERF1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TRERF1 MUTATED                                               0
  TRERF1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TRERF1 MUTATED                                0
  TRERF1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TRERF1 MUTATED                                    0
  TRERF1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TRERF1 MUTATED                              0                             0
  TRERF1 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TRERF1 MUTATED                                               0
  TRERF1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TRERF1 MUTATED                              0
  TRERF1 WILD-TYPE                            9
D52V9, multiclass
                                                    clus
vv                                                   TRERF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   TRERF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     1  17
  TRERF1 WILD-TYPE  19 443
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      1   17
  TRERF1 WILD-TYPE   19  443
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO               1               19
  YES             17              443
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, continuous
                  vv
clus                R0  R1  R2  RX
  TRERF1 MUTATED    10   1   1   1
  TRERF1 WILD-TYPE 300  10   3  24
D52V13, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  R0             10              300
  R1              1               10
  R2              1                3
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRERF1 MUTATED                                  0     1
  TRERF1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRERF1 MUTATED                           0    14
  TRERF1 WILD-TYPE                        29   363
D52V14, multiclass
                                  clus
vv                                 TRERF1 MUTATED TRERF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        14              363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     1  11
  TRERF1 WILD-TYPE   5 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      1   11
  TRERF1 WILD-TYPE    5  338
                        clus
vv                       TRERF1 MUTATED TRERF1 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(53) Variable = DSC2 MUTATION ANALYSIS
D53V1, survival
                sevent
clus2              0   1
  DSC2 MUTATED    15   5
  DSC2 WILD-TYPE 300 136
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            436 
  DSC2 MUTATED DSC2 WILD-TYPE 
             5            136 
$`DSC2 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-44-2657 TCGA-44-7662 TCGA-44-7670 TCGA-49-6742 
       19.96        14.01        13.15         7.17        29.00        14.63 
TCGA-49-6743 TCGA-53-7626 TCGA-55-7576 TCGA-55-8207 TCGA-55-8507 TCGA-55-8508 
       12.13        30.54         1.32         2.17         0.26         0.49 
TCGA-69-A59K TCGA-78-7542 TCGA-86-8073 TCGA-97-7554 TCGA-97-7938 TCGA-MP-A4TC 
        7.04        10.55        24.33        25.48         0.59         2.43 
TCGA-NJ-A4YI TCGA-NJ-A4YP 
        0.13         1.64 

$`DSC2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        46.98        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       14.60        19.46        12.03        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
       32.84         8.81        29.46        29.75        55.89        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        25.61         7.59        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.36        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
       13.45         4.24         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
       31.20         8.02        53.33        10.75        39.35        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
       31.69        64.60        63.52        43.79         5.95         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YQ 
       14.10        19.13        73.91        71.05        62.60        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  DSC2 MUTATED DSC2 WILD-TYPE 
          0.13           0.00 
  DSC2 MUTATED DSC2 WILD-TYPE 
         30.54         223.96 
  DSC2 MUTATED DSC2 WILD-TYPE 
         8.860         18.655 
[1] "0.1 - 30.5 (8.9)"   "0.0 - 224.0 (18.7)"
[1] "hr=" "2.1"
D53V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DSC2 MUTATED         0        2        8         3         2          5
  DSC2 WILD-TYPE       4      121      125        43        65         65
                vv
clus             STAGE IIIB STAGE IV
  DSC2 MUTATED            0        0
  DSC2 WILD-TYPE         11       25
D53V3, multiclass
            clus
vv           DSC2 MUTATED DSC2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              8            125
  STAGE IIA             3             43
  STAGE IIB             2             65
  STAGE IIIA            5             65
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSC2 MUTATED     6  13   1   0
  DSC2 WILD-TYPE 149 248  42  18
D53V4, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  T1            6            149
  T2           13            248
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  DSC2 MUTATED    10   4     5
  DSC2 WILD-TYPE 297  85    67
D53V5, multiclass
       clus
vv      DSC2 MUTATED DSC2 WILD-TYPE
  N0              10            297
  N1               4             85
  N2+N3            5             67
[1] 3 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
  DSC2 MUTATED    14   0
  DSC2 WILD-TYPE 313  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     14    0
  DSC2 WILD-TYPE  313   23
   clus
vv  DSC2 MUTATED DSC2 WILD-TYPE
  0           14            313
  1            0             23
[1] 2 2
[1] FALSE
D53V7, binary
                cls
clus               0   1
  DSC2 MUTATED     9  11
  DSC2 WILD-TYPE 250 210
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      9   11
  DSC2 WILD-TYPE  250  210
        clus
vv       DSC2 MUTATED DSC2 WILD-TYPE
  FEMALE            9            250
  MALE             11            210
[1] 2 2
[1] FALSE
D53V8, continuous
[1] "Remove cluster labels:" "DSC2 MUTATED"          
clus
  DSC2 MUTATED DSC2 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8511     TCGA-55-8512     TCGA-55-8619 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5778     TCGA-69-7974 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-69-8254     TCGA-71-6725     TCGA-71-8520     TCGA-73-4659 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4676 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8055     TCGA-86-8056 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"DSC2 WILD-TYPE" "DSC2 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DSC2 MUTATED                            1                                 3
  DSC2 WILD-TYPE                         17                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DSC2 MUTATED                                                    8
  DSC2 WILD-TYPE                                                286
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DSC2 MUTATED                                            0
  DSC2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DSC2 MUTATED                                               2
  DSC2 WILD-TYPE                                            17
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  DSC2 MUTATED                                1
  DSC2 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  DSC2 MUTATED                                    0
  DSC2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DSC2 MUTATED                              0                             3
  DSC2 WILD-TYPE                            2                            19
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DSC2 MUTATED                                               0
  DSC2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  DSC2 MUTATED                              2
  DSC2 WILD-TYPE                            7
D53V9, multiclass
                                                    clus
vv                                                   DSC2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 2
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 3
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  2
                                                    clus
vv                                                   DSC2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  19
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                cls
clus               0   1
  DSC2 MUTATED     0  20
  DSC2 WILD-TYPE  20 440
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      0   20
  DSC2 WILD-TYPE   20  440
     clus
vv    DSC2 MUTATED DSC2 WILD-TYPE
  NO             0             20
  YES           20            440
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, continuous
                vv
clus              R0  R1  R2  RX
  DSC2 MUTATED    13   0   0   1
  DSC2 WILD-TYPE 297  11   4  24
D53V13, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  R0           13            297
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSC2 MUTATED                                  0     0
  DSC2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSC2 MUTATED                           3    15
  DSC2 WILD-TYPE                        26   362
D53V14, multiclass
                                  clus
vv                                 DSC2 MUTATED DSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   3             26
  WHITE                                      15            362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                cls
clus               0   1
  DSC2 MUTATED     1  14
  DSC2 WILD-TYPE   5 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      1   14
  DSC2 WILD-TYPE    5  335
                        clus
vv                       DSC2 MUTATED DSC2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           14            335
[1] 2 2
[1] FALSE

Clustering(54) Variable = BTK MUTATION ANALYSIS
D54V1, survival
               sevent
clus2             0   1
  BTK MUTATED    11   3
  BTK WILD-TYPE 304 138
  BTK MUTATED BTK WILD-TYPE 
           14           442 
  BTK MUTATED BTK WILD-TYPE 
            3           138 
$`BTK MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4432 TCGA-44-3398 TCGA-44-7661 TCGA-55-7907 
       19.96        37.02        25.02        38.24        12.03         0.53 
TCGA-55-8208 TCGA-55-A48X TCGA-55-A490 TCGA-55-A4DF TCGA-64-1681 TCGA-73-4662 
       22.16        22.65         1.58        20.19        38.37        29.98 
TCGA-MP-A4T4 TCGA-NJ-A55O 
       86.04         0.43 

$`BTK WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        55.43        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26        19.82        59.11 

  BTK MUTATED BTK WILD-TYPE 
         0.43          0.00 
  BTK MUTATED BTK WILD-TYPE 
        86.04        223.96 
  BTK MUTATED BTK WILD-TYPE 
       22.405        17.735 
[1] "0.4 - 86.0 (22.4)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "1.6"
D54V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BTK MUTATED         0        6        4         4         2          0
  BTK WILD-TYPE       4      117      129        42        65         70
               vv
clus            STAGE IIIB STAGE IV
  BTK MUTATED            0        0
  BTK WILD-TYPE         11       25
D54V3, multiclass
            clus
vv           BTK MUTATED BTK WILD-TYPE
  STAGE I              0             4
  STAGE IA             6           117
  STAGE IB             4           129
  STAGE IIA            4            42
  STAGE IIB            2            65
  STAGE IIIA           0            70
  STAGE IIIB           0            11
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  BTK MUTATED     8   8   0   0
  BTK WILD-TYPE 147 253  43  18
D54V4, multiclass
    clus
vv   BTK MUTATED BTK WILD-TYPE
  T1           8           147
  T2           8           253
  T3           0            43
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  BTK MUTATED    11   5     0
  BTK WILD-TYPE 296  84    72
D54V5, multiclass
       clus
vv      BTK MUTATED BTK WILD-TYPE
  N0             11           296
  N1              5            84
  N2+N3           0            72
[1] 3 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
  BTK MUTATED    13   0
  BTK WILD-TYPE 314  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED     13    0
  BTK WILD-TYPE  314   23
   clus
vv  BTK MUTATED BTK WILD-TYPE
  0          13           314
  1           0            23
[1] 2 2
[1] FALSE
D54V7, binary
               cls
clus              0   1
  BTK MUTATED    11   5
  BTK WILD-TYPE 248 216
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED     11    5
  BTK WILD-TYPE  248  216
        clus
vv       BTK MUTATED BTK WILD-TYPE
  FEMALE          11           248
  MALE             5           216
[1] 2 2
[1] FALSE
D54V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BTK MUTATED                            0                                 3
  BTK WILD-TYPE                         18                                99
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BTK MUTATED                                                   12
  BTK WILD-TYPE                                                282
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BTK MUTATED                                            0
  BTK WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BTK MUTATED                                               0
  BTK WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  BTK MUTATED                                0
  BTK WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  BTK MUTATED                                    0                            0
  BTK WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  BTK MUTATED                               0
  BTK WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BTK MUTATED                                               0
  BTK WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  BTK MUTATED                              1
  BTK WILD-TYPE                            8
D54V9, multiclass
                                                    clus
vv                                                   BTK MUTATED BTK WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            3            99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          12           282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 1             8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
               cls
clus              0   1
  BTK MUTATED     0  16
  BTK WILD-TYPE  20 444
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      0   16
  BTK WILD-TYPE   20  444
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO            0            20
  YES          16           444
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, continuous
               vv
clus             R0  R1  R2  RX
  BTK MUTATED    14   0   0   0
  BTK WILD-TYPE 296  11   4  25
D54V13, multiclass
    clus
vv   BTK MUTATED BTK WILD-TYPE
  R0          14           296
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTK MUTATED                                  0     0
  BTK WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  BTK MUTATED                           0    11
  BTK WILD-TYPE                        29   366
D54V14, multiclass
                                  clus
vv                                 BTK MUTATED BTK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                     11           366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
               cls
clus              0   1
  BTK MUTATED     0  10
  BTK WILD-TYPE   6 339
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      0   10
  BTK WILD-TYPE    6  339
                        clus
vv                       BTK MUTATED BTK WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          10           339
[1] 2 2
[1] FALSE

Clustering(55) Variable = KIF18B MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  KIF18B MUTATED     3   1
  KIF18B WILD-TYPE 312 140
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              452 
  KIF18B MUTATED KIF18B WILD-TYPE 
               1              140 
$`KIF18B MUTATED`
TCGA-05-4250 TCGA-05-4424 TCGA-64-1676 TCGA-67-3771 
        3.98        30.02        56.81        20.05 

$`KIF18B WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  KIF18B MUTATED KIF18B WILD-TYPE 
            3.98             0.00 
  KIF18B MUTATED KIF18B WILD-TYPE 
           56.81           223.96 
  KIF18B MUTATED KIF18B WILD-TYPE 
          25.035           17.950 
[1] "4.0 - 56.8 (25.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D55V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KIF18B MUTATED         0        2        0         0         1          1
  KIF18B WILD-TYPE       4      121      133        46        66         69
                  vv
clus               STAGE IIIB STAGE IV
  KIF18B MUTATED            0        0
  KIF18B WILD-TYPE         11       25
D55V3, multiclass
            clus
vv           KIF18B MUTATED KIF18B WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                0              133
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF18B MUTATED     2   0   2   0
  KIF18B WILD-TYPE 153 261  41  18
D55V4, multiclass
    clus
vv   KIF18B MUTATED KIF18B WILD-TYPE
  T1              2              153
  T2              0              261
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  KIF18B MUTATED     3   1     0
  KIF18B WILD-TYPE 304  88    72
D55V5, multiclass
       clus
vv      KIF18B MUTATED KIF18B WILD-TYPE
  N0                 3              304
  N1                 1               88
  N2+N3              0               72
[1] 3 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
  KIF18B MUTATED     4   0
  KIF18B WILD-TYPE 323  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      4    0
  KIF18B WILD-TYPE  323   23
   clus
vv  KIF18B MUTATED KIF18B WILD-TYPE
  0              4              323
  1              0               23
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  KIF18B MUTATED     2   2
  KIF18B WILD-TYPE 257 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      2    2
  KIF18B WILD-TYPE  257  219
        clus
vv       KIF18B MUTATED KIF18B WILD-TYPE
  FEMALE              2              257
  MALE                2              219
[1] 2 2
[1] FALSE
D55V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KIF18B MUTATED                            0                                 1
  KIF18B WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KIF18B MUTATED                                                    3
  KIF18B WILD-TYPE                                                291
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KIF18B MUTATED                                            0
  KIF18B WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KIF18B MUTATED                                               0
  KIF18B WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  KIF18B MUTATED                                0
  KIF18B WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  KIF18B MUTATED                                    0
  KIF18B WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KIF18B MUTATED                              0                             0
  KIF18B WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KIF18B MUTATED                                               0
  KIF18B WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  KIF18B MUTATED                              0
  KIF18B WILD-TYPE                            9
D55V9, multiclass
                                                    clus
vv                                                   KIF18B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   KIF18B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                  cls
clus                 0   1
  KIF18B MUTATED     0   4
  KIF18B WILD-TYPE  20 456
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      0    4
  KIF18B WILD-TYPE   20  456
     clus
vv    KIF18B MUTATED KIF18B WILD-TYPE
  NO               0               20
  YES              4              456
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, continuous
[1] "Remove cluster labels:" "KIF18B MUTATED"        
clus
  KIF18B MUTATED KIF18B WILD-TYPE 
               1              256 
      TCGA-05-4384       TCGA-05-4390       TCGA-05-4396       TCGA-05-4405 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-4410       TCGA-05-4415       TCGA-05-4417       TCGA-05-4427 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-4433       TCGA-05-5420       TCGA-05-5423       TCGA-05-5425 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-5428       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-4625       TCGA-38-4626       TCGA-38-7271       TCGA-38-A44F 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-2656       TCGA-44-2657       TCGA-44-3396       TCGA-44-3398 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-3918       TCGA-44-4112       TCGA-44-5644       TCGA-44-5645 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6145       TCGA-44-6147       TCGA-44-6148 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6774       TCGA-44-6775       TCGA-44-6776       TCGA-44-6777 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6778       TCGA-44-6779       TCGA-44-7659       TCGA-44-7660 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7661       TCGA-44-7662       TCGA-44-7667       TCGA-44-7669 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7670       TCGA-44-7672       TCGA-44-8117       TCGA-44-8119 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A47F       TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4494       TCGA-49-4505       TCGA-53-7624 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-53-7626       TCGA-53-7813       TCGA-53-A4EZ       TCGA-55-1592 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-1595       TCGA-55-5899       TCGA-55-6642       TCGA-55-6712 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6971       TCGA-55-7227       TCGA-55-7283       TCGA-55-7570 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7574       TCGA-55-7576       TCGA-55-7724       TCGA-55-7725 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7728       TCGA-55-7907       TCGA-55-7910 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7911       TCGA-55-7914       TCGA-55-8089       TCGA-55-8092 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8094       TCGA-55-8096       TCGA-55-8097       TCGA-55-8205 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8299       TCGA-55-8301       TCGA-55-8302       TCGA-55-8506 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8511       TCGA-55-8512       TCGA-55-8514 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8615       TCGA-55-8620       TCGA-55-8621       TCGA-55-A48X 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A493       TCGA-55-A494       TCGA-62-8398 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5774       TCGA-64-5775 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-5778       TCGA-64-5779       TCGA-64-5781       TCGA-69-7761 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7763       TCGA-69-7764       TCGA-69-7765       TCGA-69-7974 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7979       TCGA-69-8253       TCGA-69-8255       TCGA-69-A59K 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4675       TCGA-73-4676       TCGA-73-7498 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-75-6214       TCGA-75-7025       TCGA-75-7027       TCGA-75-7031 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7145       TCGA-78-7146       TCGA-78-7147       TCGA-78-7148 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7149       TCGA-78-7150       TCGA-78-7152       TCGA-78-7153 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7154       TCGA-78-7155       TCGA-78-7156       TCGA-78-7158 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7159       TCGA-78-7160       TCGA-78-7161       TCGA-78-7162 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7163       TCGA-78-7166       TCGA-78-7167       TCGA-78-7220 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7535       TCGA-78-7536       TCGA-78-7537       TCGA-78-7539 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7542       TCGA-78-7633       TCGA-78-8640       TCGA-78-8648 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-8655       TCGA-78-8660       TCGA-78-8662       TCGA-80-5607 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-80-5608       TCGA-83-5908       TCGA-86-6851       TCGA-86-7711 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-8054       TCGA-86-8055 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8073       TCGA-86-8074       TCGA-86-8281 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8669       TCGA-86-8673 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8674       TCGA-86-A456       TCGA-91-6829       TCGA-91-6830 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6836       TCGA-91-6840       TCGA-91-6849       TCGA-91-8499 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-A4BC       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JQ       TCGA-95-7043 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7562       TCGA-95-7567       TCGA-95-7944       TCGA-95-7947 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7948       TCGA-95-A4VK       TCGA-95-A4VN       TCGA-95-A4VP 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7546       TCGA-97-7553       TCGA-97-7554       TCGA-97-7941 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8171       TCGA-97-8172       TCGA-97-8174       TCGA-97-8176 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8179       TCGA-97-A4LX       TCGA-97-A4M0       TCGA-97-A4M1 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M3       TCGA-97-A4M5       TCGA-97-A4M7 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-J2-8194       TCGA-J2-A4AD       TCGA-J2-A4AG       TCGA-L4-A4E5 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-L4-A4E6       TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T7       TCGA-MP-A4T8 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC       TCGA-MP-A4TE 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A4TK 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A5C7       TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-O1-A52J 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  KIF18B MUTATED     2   1   1   0
  KIF18B WILD-TYPE 308  10   3  25
D55V13, multiclass
    clus
vv   KIF18B MUTATED KIF18B WILD-TYPE
  R0              2              308
  R1              1               10
  R2              1                3
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF18B MUTATED                                  0     0
  KIF18B WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF18B MUTATED                           1     1
  KIF18B WILD-TYPE                        28   376
D55V14, multiclass
[1] "Remove cluster labels:" "KIF18B MUTATED"        
clus
  KIF18B MUTATED KIF18B WILD-TYPE 
               2              412 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-38-4625 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-4626       TCGA-38-4627       TCGA-38-4628       TCGA-38-4629 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-4630       TCGA-38-4631       TCGA-38-4632       TCGA-38-6178 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-7271       TCGA-38-A44F       TCGA-44-2656       TCGA-44-2657 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-2661       TCGA-44-2665       TCGA-44-3396       TCGA-44-3398 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-44-5643 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-5644       TCGA-44-5645       TCGA-44-6144       TCGA-44-6145 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6146       TCGA-44-6147       TCGA-44-6148       TCGA-44-6774 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6775       TCGA-44-6776       TCGA-44-6777       TCGA-44-6778 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6779       TCGA-44-7659       TCGA-44-7660       TCGA-44-7661 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7662       TCGA-44-7667       TCGA-44-7669       TCGA-44-7670 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7671       TCGA-44-7672       TCGA-44-8117       TCGA-44-8119 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A47F       TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4488       TCGA-49-4490 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4494       TCGA-49-4501       TCGA-49-4505       TCGA-49-4506 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4507       TCGA-49-4510       TCGA-49-4512       TCGA-49-4514 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-49-6745 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-6761       TCGA-49-6767       TCGA-50-5044       TCGA-50-5045 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5049       TCGA-50-5051       TCGA-50-5055       TCGA-50-5066 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5068       TCGA-50-5072       TCGA-50-5930       TCGA-50-5931 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5932       TCGA-50-5933       TCGA-50-5935       TCGA-50-5936 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5939       TCGA-50-5941       TCGA-50-5942       TCGA-50-5944 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5946       TCGA-50-6590       TCGA-50-6591       TCGA-50-6592 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-6593       TCGA-50-6594       TCGA-50-6595       TCGA-50-6597 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-6673       TCGA-50-7109       TCGA-50-8457       TCGA-50-8459 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-8460       TCGA-53-7624       TCGA-53-7626       TCGA-53-7813 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-1592       TCGA-55-1595       TCGA-55-5899 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6543       TCGA-55-6642       TCGA-55-6712       TCGA-55-6968 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6969       TCGA-55-6970       TCGA-55-6971       TCGA-55-6972 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6975       TCGA-55-6978       TCGA-55-6979       TCGA-55-6980 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6981       TCGA-55-6982       TCGA-55-6983       TCGA-55-6984 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6985       TCGA-55-6986       TCGA-55-6987       TCGA-55-7227 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7281       TCGA-55-7283       TCGA-55-7284       TCGA-55-7570 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7573       TCGA-55-7574       TCGA-55-7576       TCGA-55-7724 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7727       TCGA-55-7816 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7903       TCGA-55-7907       TCGA-55-7910       TCGA-55-7911 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7914       TCGA-55-7994       TCGA-55-7995       TCGA-55-8085 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8087       TCGA-55-8089       TCGA-55-8090       TCGA-55-8091 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8096       TCGA-55-8097 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8206 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8207       TCGA-55-8208       TCGA-55-8299       TCGA-55-8301 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8302       TCGA-55-8505       TCGA-55-8506       TCGA-55-8507 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8510       TCGA-55-8511       TCGA-55-8512 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8513       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8616       TCGA-55-8619       TCGA-55-8620       TCGA-55-8621 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A493       TCGA-55-A494 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A4DF       TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1679 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5774       TCGA-64-5775       TCGA-64-5778 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-5779       TCGA-64-5781       TCGA-64-5815       TCGA-67-3772 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-67-3773       TCGA-67-4679       TCGA-67-6215       TCGA-67-6216 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-67-6217       TCGA-69-7760       TCGA-69-7761       TCGA-69-7763 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7764       TCGA-69-7765       TCGA-69-7973       TCGA-69-7974 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7978       TCGA-69-7979       TCGA-69-7980       TCGA-69-8253 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-8254       TCGA-69-8255       TCGA-69-A59K       TCGA-71-6725 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4658       TCGA-73-4659       TCGA-73-4662 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4666       TCGA-73-4668       TCGA-73-4670       TCGA-73-4675 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4676       TCGA-73-4677       TCGA-73-7498       TCGA-73-7499 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7143       TCGA-78-7145       TCGA-78-7146       TCGA-78-7147 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7148       TCGA-78-7149       TCGA-78-7150       TCGA-78-7152 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7153       TCGA-78-7154       TCGA-78-7155       TCGA-78-7156 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7158       TCGA-78-7159       TCGA-78-7160       TCGA-78-7161 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7162       TCGA-78-7163       TCGA-78-7166       TCGA-78-7167 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7220       TCGA-78-7535       TCGA-78-7536       TCGA-78-7539 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7540       TCGA-78-7542       TCGA-78-7633       TCGA-83-5908 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-6562       TCGA-86-6851       TCGA-86-7701       TCGA-86-7711 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7953       TCGA-86-7954 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7955       TCGA-86-8054       TCGA-86-8055       TCGA-86-8056 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8280       TCGA-86-8281 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8585       TCGA-86-8668 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8669       TCGA-86-8671       TCGA-86-8672       TCGA-86-8673 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8674       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-A4P8       TCGA-91-6828       TCGA-91-6829       TCGA-91-6830 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6831       TCGA-91-6835       TCGA-91-6836       TCGA-91-6840 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6847       TCGA-91-6848       TCGA-91-6849       TCGA-91-7771 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-8496       TCGA-91-8497       TCGA-91-8499       TCGA-91-A4BC 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-A4BD       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JP       TCGA-93-A4JQ 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7039       TCGA-95-7043       TCGA-95-7562       TCGA-95-7567 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7944       TCGA-95-7947       TCGA-95-7948       TCGA-95-8039 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-8494       TCGA-95-A4VK       TCGA-95-A4VN       TCGA-95-A4VP 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7546       TCGA-97-7547       TCGA-97-7552       TCGA-97-7553 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7554       TCGA-97-7937       TCGA-97-7938       TCGA-97-7941 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8171       TCGA-97-8172       TCGA-97-8174       TCGA-97-8175 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8176       TCGA-97-8177       TCGA-97-8179       TCGA-97-8552 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4LX       TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M2 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4M3       TCGA-97-A4M5       TCGA-97-A4M6       TCGA-97-A4M7 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-99-8033       TCGA-J2-8192       TCGA-J2-8194       TCGA-J2-A4AD 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-J2-A4AE       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1       TCGA-MN-A4N4 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MN-A4N5       TCGA-MP-A4SW       TCGA-MP-A4SY       TCGA-MP-A4T2 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T9       TCGA-MP-A4TA 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TC       TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A5C7       TCGA-NJ-A4YF 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-NJ-A4YP       TCGA-NJ-A4YQ 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-NJ-A55A       TCGA-NJ-A55O       TCGA-NJ-A55R       TCGA-O1-A52J 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
D55V15, binary
                  cls
clus                 0   1
  KIF18B MUTATED     0   2
  KIF18B WILD-TYPE   6 347
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      0    2
  KIF18B WILD-TYPE    6  347
                        clus
vv                       KIF18B MUTATED KIF18B WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              2              347
[1] 2 2
[1] FALSE

Clustering(56) Variable = WDR66 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2               0   1
  WDR66 MUTATED     8   5
  WDR66 WILD-TYPE 307 136
  WDR66 MUTATED WDR66 WILD-TYPE 
             13             443 
  WDR66 MUTATED WDR66 WILD-TYPE 
              5             136 
$`WDR66 MUTATED`
TCGA-05-4420 TCGA-35-5375 TCGA-53-7624 TCGA-55-A48X TCGA-62-8399 TCGA-67-3771 
       29.98         8.68        34.29        22.65        88.64        20.05 
TCGA-78-7155 TCGA-78-7536 TCGA-78-7539 TCGA-78-8662 TCGA-86-8056 TCGA-99-8025 
       38.50         8.02        10.75       110.50         4.57        34.85 
TCGA-O1-A52J 
       59.11 

$`WDR66 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       19.99         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       31.20        53.33        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        10.55        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       16.70        24.49         4.08        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        1.64        29.13         0.26         0.43        19.82 

  WDR66 MUTATED WDR66 WILD-TYPE 
           4.57            0.00 
  WDR66 MUTATED WDR66 WILD-TYPE 
         110.50          223.96 
  WDR66 MUTATED WDR66 WILD-TYPE 
          29.98           17.75 
[1] "4.6 - 110.5 (30.0)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.4"
D56V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  WDR66 MUTATED         0        2        4         2         0          5
  WDR66 WILD-TYPE       4      121      129        44        67         65
                 vv
clus              STAGE IIIB STAGE IV
  WDR66 MUTATED            0        1
  WDR66 WILD-TYPE         11       24
D56V3, multiclass
            clus
vv           WDR66 MUTATED WDR66 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               4             129
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             5              65
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR66 MUTATED     3   9   1   1
  WDR66 WILD-TYPE 152 252  42  17
D56V4, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  T1             3             152
  T2             9             252
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  WDR66 MUTATED     9   1     4
  WDR66 WILD-TYPE 298  88    68
D56V5, multiclass
       clus
vv      WDR66 MUTATED WDR66 WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             4              68
[1] 3 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
  WDR66 MUTATED    12   1
  WDR66 WILD-TYPE 315  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     12    1
  WDR66 WILD-TYPE  315   22
   clus
vv  WDR66 MUTATED WDR66 WILD-TYPE
  0            12             315
  1             1              22
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus                0   1
  WDR66 MUTATED     8   6
  WDR66 WILD-TYPE 251 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      8    6
  WDR66 WILD-TYPE  251  215
        clus
vv       WDR66 MUTATED WDR66 WILD-TYPE
  FEMALE             8             251
  MALE               6             215
[1] 2 2
[1] FALSE
D56V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  WDR66 MUTATED                            0                                 3
  WDR66 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  WDR66 MUTATED                                                   10
  WDR66 WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  WDR66 MUTATED                                            0
  WDR66 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  WDR66 MUTATED                                               0
  WDR66 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  WDR66 MUTATED                                0
  WDR66 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  WDR66 MUTATED                                    0
  WDR66 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  WDR66 MUTATED                              0                             1
  WDR66 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  WDR66 MUTATED                                               0
  WDR66 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  WDR66 MUTATED                              0
  WDR66 WILD-TYPE                            9
D56V9, multiclass
                                                    clus
vv                                                   WDR66 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   WDR66 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                 cls
clus                0   1
  WDR66 MUTATED     1  13
  WDR66 WILD-TYPE  19 447
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      1   13
  WDR66 WILD-TYPE   19  447
     clus
vv    WDR66 MUTATED WDR66 WILD-TYPE
  NO              1              19
  YES            13             447
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, continuous
                 vv
clus               R0  R1  R2  RX
  WDR66 MUTATED    13   0   0   0
  WDR66 WILD-TYPE 297  11   4  25
D56V13, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  R0            13             297
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR66 MUTATED                                  0     0
  WDR66 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR66 MUTATED                           2     9
  WDR66 WILD-TYPE                        27   368
D56V14, multiclass
                                  clus
vv                                 WDR66 MUTATED WDR66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                 cls
clus                0   1
  WDR66 MUTATED     1   7
  WDR66 WILD-TYPE   5 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      1    7
  WDR66 WILD-TYPE    5  342
                        clus
vv                       WDR66 MUTATED WDR66 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(57) Variable = PTEN MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     5   2
  PTEN WILD-TYPE 310 139
  PTEN MUTATED PTEN WILD-TYPE 
             7            449 
  PTEN MUTATED PTEN WILD-TYPE 
             2            139 
$`PTEN MUTATED`
TCGA-44-3398 TCGA-44-7661 TCGA-44-7662 TCGA-73-4658 TCGA-78-7155 TCGA-86-A4JF 
       38.24        12.03         7.17        52.60        38.50        17.62 
TCGA-91-8499 
        1.18 

$`PTEN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        14.60        19.46        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01         0.10        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
        7.36         1.15        16.18        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  PTEN MUTATED PTEN WILD-TYPE 
          1.18           0.00 
  PTEN MUTATED PTEN WILD-TYPE 
         52.60         223.96 
  PTEN MUTATED PTEN WILD-TYPE 
         17.62          18.08 
[1] "1.2 - 52.6 (17.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D57V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PTEN MUTATED         0        2        4         0         1          0
  PTEN WILD-TYPE       4      121      129        46        66         70
                vv
clus             STAGE IIIB STAGE IV
  PTEN MUTATED            0        0
  PTEN WILD-TYPE         11       25
D57V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              4            129
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   4   1   0
  PTEN WILD-TYPE 153 257  42  18
D57V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            2            153
  T2            4            257
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  PTEN MUTATED     7   0     0
  PTEN WILD-TYPE 300  89    72
D57V5, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  N0               7            300
  N1               0             89
  N2+N3            0             72
[1] 3 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
  PTEN MUTATED     5   0
  PTEN WILD-TYPE 322  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE  322   23
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            5            322
  1            0             23
[1] 2 2
[1] FALSE
D57V7, binary
                cls
clus               0   1
  PTEN MUTATED     4   3
  PTEN WILD-TYPE 255 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    3
  PTEN WILD-TYPE  255  218
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4            255
  MALE              3            218
[1] 2 2
[1] FALSE
D57V8, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7711 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7954     TCGA-86-7955 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8074     TCGA-86-8075 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8281 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PTEN MUTATED                            0                                 0
  PTEN WILD-TYPE                         18                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTEN MUTATED                                                    7
  PTEN WILD-TYPE                                                287
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PTEN MUTATED                                            0
  PTEN WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PTEN MUTATED                                               0
  PTEN WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  PTEN MUTATED                                0
  PTEN WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  PTEN MUTATED                                    0
  PTEN WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PTEN MUTATED                              0                             0
  PTEN WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PTEN MUTATED                                               0
  PTEN WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  PTEN MUTATED                              0
  PTEN WILD-TYPE                            9
D57V9, multiclass
                                                    clus
vv                                                   PTEN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   PTEN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                cls
clus               0   1
  PTEN MUTATED     0   7
  PTEN WILD-TYPE  20 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    7
  PTEN WILD-TYPE   20  453
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             0             20
  YES            7            453
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, continuous
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     4   0   0   0
  PTEN WILD-TYPE 306  11   4  25
D57V13, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     0
  PTEN WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           0     7
  PTEN WILD-TYPE                        29   370
D57V14, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                cls
clus               0   1
  PTEN MUTATED     0   6
  PTEN WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    6
  PTEN WILD-TYPE    6  343
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(58) Variable = LTBP1 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  LTBP1 MUTATED    31  12
  LTBP1 WILD-TYPE 284 129
  LTBP1 MUTATED LTBP1 WILD-TYPE 
             43             413 
  LTBP1 MUTATED LTBP1 WILD-TYPE 
             12             129 
$`LTBP1 MUTATED`
TCGA-05-4390 TCGA-05-4427 TCGA-05-4432 TCGA-35-4123 TCGA-38-4625 TCGA-38-4632 
       37.02        26.01        25.02         5.98        97.74        44.61 
TCGA-44-2656 TCGA-44-6778 TCGA-44-6779 TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 
       46.98        61.28        16.44        29.00         3.25        15.98 
TCGA-49-4488 TCGA-49-6767 TCGA-55-1595 TCGA-55-6968 TCGA-55-8092 TCGA-55-8207 
       28.57        22.26        48.62        42.51         5.06         2.17 
TCGA-55-8208 TCGA-55-8616 TCGA-55-A4DF TCGA-64-1679 TCGA-64-5781 TCGA-67-3771 
       22.16         1.58        20.19        55.43        51.25        20.05 
TCGA-67-3773 TCGA-69-7765 TCGA-69-A59K TCGA-78-7155 TCGA-78-7159 TCGA-78-8662 
       14.04         5.42         7.04        38.50        64.90       110.50 
TCGA-86-6851 TCGA-86-8073 TCGA-91-6830 TCGA-95-7043 TCGA-97-7937 TCGA-97-7938 
        5.88        24.33         1.97         1.22         5.95         0.59 
TCGA-97-8179 TCGA-99-8028 TCGA-99-8032 TCGA-MP-A4T4 TCGA-MP-A4TA TCGA-MP-A4TE 
       14.30        36.76         1.45        86.04        31.23        29.46 
TCGA-NJ-A4YP 
        1.64 

$`LTBP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       21.99        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        8.68       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       11.64        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
       17.59        23.64        12.66         8.55        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05         2.86         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        20.65        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       28.41        28.47        18.84         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        22.68        13.61         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        5.88        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       10.55        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62        41.36        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        43.79        25.48         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       17.92         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 
       20.84        18.67        20.68        24.56        34.85         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH 
        5.29        41.59         2.43        10.09        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  LTBP1 MUTATED LTBP1 WILD-TYPE 
           0.59            0.00 
  LTBP1 MUTATED LTBP1 WILD-TYPE 
         110.50          223.96 
  LTBP1 MUTATED LTBP1 WILD-TYPE 
          22.26           17.72 
[1] "0.6 - 110.5 (22.3)" "0.0 - 224.0 (17.7)"
[1] "hr=" "1.5"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LTBP1 MUTATED         0       14       15         4         8          2
  LTBP1 WILD-TYPE       4      109      118        42        59         68
                 vv
clus              STAGE IIIB STAGE IV
  LTBP1 MUTATED            0        3
  LTBP1 WILD-TYPE         11       22
D58V3, multiclass
            clus
vv           LTBP1 MUTATED LTBP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA              14             109
  STAGE IB              15             118
  STAGE IIA              4              42
  STAGE IIB              8              59
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               3              22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LTBP1 MUTATED    19  21   5   1
  LTBP1 WILD-TYPE 136 240  38  17
D58V4, multiclass
    clus
vv   LTBP1 MUTATED LTBP1 WILD-TYPE
  T1            19             136
  T2            21             240
  T3             5              38
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  LTBP1 MUTATED    35   8     2
  LTBP1 WILD-TYPE 272  81    70
D58V5, multiclass
       clus
vv      LTBP1 MUTATED LTBP1 WILD-TYPE
  N0               35             272
  N1                8              81
  N2+N3             2              70
[1] 3 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
  LTBP1 MUTATED    30   2
  LTBP1 WILD-TYPE 297  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP1 MUTATED     30    2
  LTBP1 WILD-TYPE  297   21
   clus
vv  LTBP1 MUTATED LTBP1 WILD-TYPE
  0            30             297
  1             2              21
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  LTBP1 MUTATED    26  20
  LTBP1 WILD-TYPE 233 201
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP1 MUTATED     26   20
  LTBP1 WILD-TYPE  233  201
        clus
vv       LTBP1 MUTATED LTBP1 WILD-TYPE
  FEMALE            26             233
  MALE              20             201
[1] 2 2
[1] FALSE
D58V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LTBP1 MUTATED                            2                                 9
  LTBP1 WILD-TYPE                         16                                93
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LTBP1 MUTATED                                                   30
  LTBP1 WILD-TYPE                                                264
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LTBP1 MUTATED                                            0
  LTBP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LTBP1 MUTATED                                               2
  LTBP1 WILD-TYPE                                            17
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  LTBP1 MUTATED                                1
  LTBP1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  LTBP1 MUTATED                                    1
  LTBP1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LTBP1 MUTATED                              0                             1
  LTBP1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LTBP1 MUTATED                                               0
  LTBP1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  LTBP1 MUTATED                              0
  LTBP1 WILD-TYPE                            9
D58V9, multiclass
                                                    clus
vv                                                   LTBP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  2
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   LTBP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             264
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   17
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                 cls
clus                0   1
  LTBP1 MUTATED     0  46
  LTBP1 WILD-TYPE  20 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP1 MUTATED      0   46
  LTBP1 WILD-TYPE   20  414
     clus
vv    LTBP1 MUTATED LTBP1 WILD-TYPE
  NO              0              20
  YES            46             414
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, continuous
                 vv
clus               R0  R1  R2  RX
  LTBP1 MUTATED    30   0   0   1
  LTBP1 WILD-TYPE 280  11   4  24
D58V13, multiclass
    clus
vv   LTBP1 MUTATED LTBP1 WILD-TYPE
  R0            30             280
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LTBP1 MUTATED                                  0     1
  LTBP1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LTBP1 MUTATED                           7    32
  LTBP1 WILD-TYPE                        22   345
D58V14, multiclass
                                  clus
vv                                 LTBP1 MUTATED LTBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    7              22
  WHITE                                       32             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                 cls
clus                0   1
  LTBP1 MUTATED     1  33
  LTBP1 WILD-TYPE   5 316
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP1 MUTATED      1   33
  LTBP1 WILD-TYPE    5  316
                        clus
vv                       LTBP1 MUTATED LTBP1 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            33             316
[1] 2 2
[1] FALSE

Clustering(59) Variable = C10ORF71 MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  C10ORF71 MUTATED     9   6
  C10ORF71 WILD-TYPE 306 135
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                15                441 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                 6                135 
$`C10ORF71 MUTATED`
TCGA-05-4382 TCGA-38-4632 TCGA-50-6592 TCGA-53-7624 TCGA-55-8301 TCGA-55-8506 
       19.96        44.61        25.55        34.29         1.45         0.36 
TCGA-55-A4DG TCGA-64-5779 TCGA-69-A59K TCGA-78-7158 TCGA-86-8585 TCGA-95-7562 
       19.99        28.41         7.04         5.88         1.15         2.86 
TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-NJ-A4YP 
       27.19        31.23         1.64 

$`C10ORF71 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 
       29.03        25.12        22.55        42.35         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        22.16        15.42         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        15.81        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        42.90        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       32.09        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
       86.04        58.85         5.49         5.29        41.59         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
              0.36               0.00 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
             44.61             223.96 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
             19.96              17.98 
[1] "0.4 - 44.6 (20.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.9"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C10ORF71 MUTATED         0        2        6         2         2          1
  C10ORF71 WILD-TYPE       4      121      127        44        65         69
                    vv
clus                 STAGE IIIB STAGE IV
  C10ORF71 MUTATED            1        2
  C10ORF71 WILD-TYPE         10       23
D59V3, multiclass
            clus
vv           C10ORF71 MUTATED C10ORF71 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  2                121
  STAGE IB                  6                127
  STAGE IIA                 2                 44
  STAGE IIB                 2                 65
  STAGE IIIA                1                 69
  STAGE IIIB                1                 10
  STAGE IV                  2                 23
[1] 8 2
[1] TRUE
[1] "dimension of 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     2  11   2   1
  C10ORF71 WILD-TYPE 153 250  41  17
D59V4, multiclass
    clus
vv   C10ORF71 MUTATED C10ORF71 WILD-TYPE
  T1                2                153
  T2               11                250
  T3                2                 41
  T4                1                 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"
                    vv
clus                  N0  N1 N2+N3
  C10ORF71 MUTATED    11   3     2
  C10ORF71 WILD-TYPE 296  86    70
D59V5, multiclass
       clus
vv      C10ORF71 MUTATED C10ORF71 WILD-TYPE
  N0                  11                296
  N1                   3                 86
  N2+N3                2                 70
[1] 3 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
  C10ORF71 MUTATED    11   2
  C10ORF71 WILD-TYPE 316  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED     11    2
  C10ORF71 WILD-TYPE  316   21
   clus
vv  C10ORF71 MUTATED C10ORF71 WILD-TYPE
  0               11                316
  1                2                 21
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                   0   1
  C10ORF71 MUTATED     6  10
  C10ORF71 WILD-TYPE 253 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED      6   10
  C10ORF71 WILD-TYPE  253  211
        clus
vv       C10ORF71 MUTATED C10ORF71 WILD-TYPE
  FEMALE                6                253
  MALE                 10                211
[1] 2 2
[1] FALSE
D59V8, continuous
[1] "Remove cluster labels:" "C10ORF71 MUTATED"      
clus
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                 1                 83 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-7283         TCGA-55-7573 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-55-7725         TCGA-55-7910         TCGA-55-7914 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8096         TCGA-55-8205 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8507         TCGA-55-8508 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8619 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-55-8620         TCGA-55-A48Z         TCGA-55-A490 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-55-A494         TCGA-62-8394         TCGA-62-8395 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-62-8397         TCGA-62-8398         TCGA-62-8399 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-62-8402         TCGA-62-A46O         TCGA-62-A46P 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-62-A46R         TCGA-62-A46S         TCGA-62-A46U 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-62-A46V         TCGA-62-A46Y         TCGA-62-A470 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-62-A471         TCGA-62-A472         TCGA-64-1677 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-64-1681         TCGA-64-5778         TCGA-69-7974 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-69-8254         TCGA-71-6725         TCGA-71-8520 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-73-4659         TCGA-73-4662         TCGA-73-4666 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-73-4668         TCGA-73-4676         TCGA-73-7498 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-73-7499         TCGA-75-5122         TCGA-83-5908 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-86-7701         TCGA-86-7711         TCGA-86-7713 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-86-7714         TCGA-86-7954         TCGA-86-7955 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-86-8055         TCGA-86-8056         TCGA-86-8074 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-86-8075         TCGA-86-8076         TCGA-86-8278 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-86-8279         TCGA-86-8281         TCGA-86-8358 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-86-8359         TCGA-86-8668         TCGA-86-8669 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-86-8671         TCGA-86-A4JF         TCGA-86-A4P7 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-91-6849         TCGA-93-7348         TCGA-93-8067 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-93-A4JN         TCGA-93-A4JO         TCGA-99-7458 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
        TCGA-MN-A4N4         TCGA-MN-A4N5 
"C10ORF71 WILD-TYPE" "C10ORF71 WILD-TYPE" 
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  C10ORF71 MUTATED                            1
  C10ORF71 WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  C10ORF71 MUTATED                                   4
  C10ORF71 WILD-TYPE                                98
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C10ORF71 MUTATED                                                    9
  C10ORF71 WILD-TYPE                                                285
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C10ORF71 MUTATED                                            0
  C10ORF71 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C10ORF71 MUTATED                                               0
  C10ORF71 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  C10ORF71 MUTATED                                0
  C10ORF71 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  C10ORF71 MUTATED                                    0
  C10ORF71 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C10ORF71 MUTATED                              0                             1
  C10ORF71 WILD-TYPE                            2                            21
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C10ORF71 MUTATED                                               1
  C10ORF71 WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  C10ORF71 MUTATED                              0
  C10ORF71 WILD-TYPE                            9
D59V9, multiclass
                                                    clus
vv                                                   C10ORF71 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   C10ORF71 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                    cls
clus                   0   1
  C10ORF71 MUTATED     1  15
  C10ORF71 WILD-TYPE  19 445
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED      1   15
  C10ORF71 WILD-TYPE   19  445
     clus
vv    C10ORF71 MUTATED C10ORF71 WILD-TYPE
  NO                 1                 19
  YES               15                445
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, continuous
                    vv
clus                  R0  R1  R2  RX
  C10ORF71 MUTATED    10   1   0   2
  C10ORF71 WILD-TYPE 300  10   4  23
D59V13, multiclass
    clus
vv   C10ORF71 MUTATED C10ORF71 WILD-TYPE
  R0               10                300
  R1                1                 10
  R2                0                  4
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF71 MUTATED                                  0     0
  C10ORF71 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C10ORF71 MUTATED                           4    10
  C10ORF71 WILD-TYPE                        25   367
D59V14, multiclass
                                  clus
vv                                 C10ORF71 MUTATED C10ORF71 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       4                 25
  WHITE                                          10                367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, binary
                    cls
clus                   0   1
  C10ORF71 MUTATED     1  12
  C10ORF71 WILD-TYPE   5 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED      1   12
  C10ORF71 WILD-TYPE    5  337
                        clus
vv                       C10ORF71 MUTATED C10ORF71 WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               12                337
[1] 2 2
[1] FALSE

Clustering(60) Variable = KLHL5 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2               0   1
  KLHL5 MUTATED    11   3
  KLHL5 WILD-TYPE 304 138
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             442 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              3             138 
$`KLHL5 MUTATED`
TCGA-44-2657 TCGA-44-3918 TCGA-44-7661 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4486 
       13.15        34.06        12.03         8.55        13.64        76.21 
TCGA-55-7284 TCGA-55-A4DG TCGA-69-8255 TCGA-86-7711 TCGA-91-6836 TCGA-95-7947 
        7.99        19.99         4.24        34.39        13.71        15.68 
TCGA-95-A4VN TCGA-NJ-A4YQ 
       18.18        29.13 

$`KLHL5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 
       44.61        14.73        26.30         4.37        46.98        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        14.60        19.46         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
       29.00        17.59        23.64        12.66         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4487 
       15.32         9.44        11.08        11.54        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 
       70.26         1.74         0.59         1.15         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        20.19         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K 
        2.30         2.93        12.56        14.01        13.45         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  KLHL5 MUTATED KLHL5 WILD-TYPE 
           4.24            0.00 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
          76.21          223.96 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
         14.695          18.100 
[1] "4.2 - 76.2 (14.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D60V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KLHL5 MUTATED         0        7        4         2         1          0
  KLHL5 WILD-TYPE       4      116      129        44        66         70
                 vv
clus              STAGE IIIB STAGE IV
  KLHL5 MUTATED            0        0
  KLHL5 WILD-TYPE         11       25
D60V3, multiclass
            clus
vv           KLHL5 MUTATED KLHL5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             116
  STAGE IB               4             129
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLHL5 MUTATED     7   6   1   0
  KLHL5 WILD-TYPE 148 255  42  18
D60V4, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  T1             7             148
  T2             6             255
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  KLHL5 MUTATED    11   2     0
  KLHL5 WILD-TYPE 296  87    72
D60V5, multiclass
       clus
vv      KLHL5 MUTATED KLHL5 WILD-TYPE
  N0               11             296
  N1                2              87
  N2+N3             0              72
[1] 3 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
  KLHL5 MUTATED    11   0
  KLHL5 WILD-TYPE 316  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED     11    0
  KLHL5 WILD-TYPE  316   23
   clus
vv  KLHL5 MUTATED KLHL5 WILD-TYPE
  0            11             316
  1             0              23
[1] 2 2
[1] FALSE
D60V7, binary
                 cls
clus                0   1
  KLHL5 MUTATED     6   8
  KLHL5 WILD-TYPE 253 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      6    8
  KLHL5 WILD-TYPE  253  213
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  FEMALE             6             253
  MALE               8             213
[1] 2 2
[1] FALSE
D60V8, continuous
[1] "Remove cluster labels:" "KLHL5 MUTATED"         
clus
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7713 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" "KLHL5 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KLHL5 MUTATED                            0                                 1
  KLHL5 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KLHL5 MUTATED                                                   10
  KLHL5 WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KLHL5 MUTATED                                            0
  KLHL5 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KLHL5 MUTATED                                               1
  KLHL5 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KLHL5 MUTATED                                0
  KLHL5 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KLHL5 MUTATED                                    0
  KLHL5 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KLHL5 MUTATED                              0                             0
  KLHL5 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KLHL5 MUTATED                                               2
  KLHL5 WILD-TYPE                                             3
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KLHL5 MUTATED                              0
  KLHL5 WILD-TYPE                            9
D60V9, multiclass
                                                    clus
vv                                                   KLHL5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  2
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   KLHL5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                 cls
clus                0   1
  KLHL5 MUTATED     0  14
  KLHL5 WILD-TYPE  20 446
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      0   14
  KLHL5 WILD-TYPE   20  446
     clus
vv    KLHL5 MUTATED KLHL5 WILD-TYPE
  NO              0              20
  YES            14             446
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, continuous
                 vv
clus               R0  R1  R2  RX
  KLHL5 MUTATED     8   0   0   1
  KLHL5 WILD-TYPE 302  11   4  24
D60V13, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLHL5 MUTATED                                  0     0
  KLHL5 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLHL5 MUTATED                           1    13
  KLHL5 WILD-TYPE                        28   364
D60V14, multiclass
                                  clus
vv                                 KLHL5 MUTATED KLHL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       13             364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                 cls
clus                0   1
  KLHL5 MUTATED     2  12
  KLHL5 WILD-TYPE   4 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      2   12
  KLHL5 WILD-TYPE    4  337
                        clus
vv                       KLHL5 MUTATED KLHL5 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(61) Variable = FAM65C MUTATION ANALYSIS
D61V1, survival
                  sevent
clus2                0   1
  FAM65C MUTATED    10   2
  FAM65C WILD-TYPE 305 139
  FAM65C MUTATED FAM65C WILD-TYPE 
              12              444 
  FAM65C MUTATED FAM65C WILD-TYPE 
               2              139 
$`FAM65C MUTATED`
TCGA-44-7667 TCGA-44-7670 TCGA-44-A47A TCGA-49-4486 TCGA-55-8506 TCGA-62-A46U 
       36.07        29.00        15.32        76.21         0.36        67.96 
TCGA-69-7978 TCGA-78-7163 TCGA-78-7220 TCGA-86-8073 TCGA-93-8067 TCGA-97-7547 
        2.30       223.96        26.53        24.33         6.12        64.60 

$`FAM65C WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        18.87        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y 
       47.80        19.53        56.71        54.35        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        7.07       104.19         8.48        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 
        2.76        21.40        18.18        19.89        31.69        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  FAM65C MUTATED FAM65C WILD-TYPE 
            0.36             0.00 
  FAM65C MUTATED FAM65C WILD-TYPE 
          223.96           214.62 
  FAM65C MUTATED FAM65C WILD-TYPE 
          27.765           17.835 
[1] "0.4 - 224.0 (27.8)" "0.0 - 214.6 (17.8)"
[1] "hr=" "3.8"
D61V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FAM65C MUTATED         0        1        5         1         4          3
  FAM65C WILD-TYPE       4      122      128        45        63         67
                  vv
clus               STAGE IIIB STAGE IV
  FAM65C MUTATED            0        0
  FAM65C WILD-TYPE         11       25
D61V3, multiclass
            clus
vv           FAM65C MUTATED FAM65C WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                5              128
  STAGE IIA               1               45
  STAGE IIB               4               63
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM65C MUTATED     2   9   3   0
  FAM65C WILD-TYPE 153 252  40  18
D61V4, multiclass
    clus
vv   FAM65C MUTATED FAM65C WILD-TYPE
  T1              2              153
  T2              9              252
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  FAM65C MUTATED     8   3     3
  FAM65C WILD-TYPE 299  86    69
D61V5, multiclass
       clus
vv      FAM65C MUTATED FAM65C WILD-TYPE
  N0                 8              299
  N1                 3               86
  N2+N3              3               69
[1] 3 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
  FAM65C MUTATED     8   0
  FAM65C WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      8    0
  FAM65C WILD-TYPE  319   23
   clus
vv  FAM65C MUTATED FAM65C WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D61V7, binary
                  cls
clus                 0   1
  FAM65C MUTATED     9   5
  FAM65C WILD-TYPE 250 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      9    5
  FAM65C WILD-TYPE  250  216
        clus
vv       FAM65C MUTATED FAM65C WILD-TYPE
  FEMALE              9              250
  MALE                5              216
[1] 2 2
[1] FALSE
D61V8, continuous
[1] "Remove cluster labels:" "FAM65C MUTATED"        
clus
  FAM65C MUTATED FAM65C WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"FAM65C WILD-TYPE" "FAM65C WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FAM65C MUTATED                            0                                 3
  FAM65C WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FAM65C MUTATED                                                    8
  FAM65C WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FAM65C MUTATED                                            0
  FAM65C WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FAM65C MUTATED                                               1
  FAM65C WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  FAM65C MUTATED                                0
  FAM65C WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  FAM65C MUTATED                                    0
  FAM65C WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FAM65C MUTATED                              0                             2
  FAM65C WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FAM65C MUTATED                                               0
  FAM65C WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  FAM65C MUTATED                              0
  FAM65C WILD-TYPE                            9
D61V9, multiclass
                                                    clus
vv                                                   FAM65C MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   FAM65C WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                  cls
clus                 0   1
  FAM65C MUTATED     1  13
  FAM65C WILD-TYPE  19 447
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      1   13
  FAM65C WILD-TYPE   19  447
     clus
vv    FAM65C MUTATED FAM65C WILD-TYPE
  NO               1               19
  YES             13              447
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, continuous
                  vv
clus                R0  R1  R2  RX
  FAM65C MUTATED     8   0   1   1
  FAM65C WILD-TYPE 302  11   3  24
D61V13, multiclass
    clus
vv   FAM65C MUTATED FAM65C WILD-TYPE
  R0              8              302
  R1              0               11
  R2              1                3
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM65C MUTATED                                  0     1
  FAM65C WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM65C MUTATED                           0    11
  FAM65C WILD-TYPE                        29   366
D61V14, multiclass
                                  clus
vv                                 FAM65C MUTATED FAM65C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        11              366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                  cls
clus                 0   1
  FAM65C MUTATED     1   9
  FAM65C WILD-TYPE   5 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      1    9
  FAM65C WILD-TYPE    5  340
                        clus
vv                       FAM65C MUTATED FAM65C WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              9              340
[1] 2 2
[1] FALSE

Clustering(62) Variable = KRTAP5-10 MUTATION ANALYSIS
D62V1, survival
                     sevent
clus2                   0   1
  KRTAP5-10 MUTATED    11   1
  KRTAP5-10 WILD-TYPE 304 140
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                 12                 444 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                  1                 140 
$`KRTAP5-10 MUTATED`
TCGA-05-5425 TCGA-44-7660 TCGA-44-7667 TCGA-49-4505 TCGA-55-8506 TCGA-55-A492 
       29.00        19.46        36.07        14.07         0.36        19.59 
TCGA-69-7979 TCGA-69-8255 TCGA-86-8073 TCGA-95-A4VN TCGA-99-7458 TCGA-NJ-A4YF 
        2.93         4.24        24.33        18.18        24.56        71.05 

$`KRTAP5-10 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       61.28        16.44        14.60        12.03         7.17        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30        12.56        14.01        13.45 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29         2.76        21.40        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
               0.36                0.00 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
              71.05              223.96 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
             19.525              17.835 
[1] "0.4 - 71.0 (19.5)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "3.4"
D62V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KRTAP5-10 MUTATED         0        3        3         1         4          1
  KRTAP5-10 WILD-TYPE       4      120      130        45        63         69
                     vv
clus                  STAGE IIIB STAGE IV
  KRTAP5-10 MUTATED            0        0
  KRTAP5-10 WILD-TYPE         11       25
D62V3, multiclass
            clus
vv           KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  STAGE I                    0                   4
  STAGE IA                   3                 120
  STAGE IB                   3                 130
  STAGE IIA                  1                  45
  STAGE IIB                  4                  63
  STAGE IIIA                 1                  69
  STAGE IIIB                 0                  11
  STAGE IV                   0                  25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KRTAP5-10 MUTATED     3   6   2   1
  KRTAP5-10 WILD-TYPE 152 255  41  17
D62V4, multiclass
    clus
vv   KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  T1                 3                 152
  T2                 6                 255
  T3                 2                  41
  T4                 1                  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"
                     vv
clus                   N0  N1 N2+N3
  KRTAP5-10 MUTATED     9   3     0
  KRTAP5-10 WILD-TYPE 298  86    72
D62V5, multiclass
       clus
vv      KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  N0                    9                 298
  N1                    3                  86
  N2+N3                 0                  72
[1] 3 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
  KRTAP5-10 MUTATED     7   0
  KRTAP5-10 WILD-TYPE 320  23
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      7    0
  KRTAP5-10 WILD-TYPE  320   23
   clus
vv  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  0                 7                 320
  1                 0                  23
[1] 2 2
[1] FALSE
D62V7, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED     8   4
  KRTAP5-10 WILD-TYPE 251 217
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      8    4
  KRTAP5-10 WILD-TYPE  251  217
        clus
vv       KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  FEMALE                 8                 251
  MALE                   4                 217
[1] 2 2
[1] FALSE
D62V8, continuous
[1] "Remove cluster labels:" "KRTAP5-10 MUTATED"     
clus
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                  1                  83 
         TCGA-35-4122          TCGA-35-4123          TCGA-35-5375 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-53-A4EZ          TCGA-55-7283          TCGA-55-7573 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-55-7725          TCGA-55-7910          TCGA-55-7914 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-55-8089          TCGA-55-8096          TCGA-55-8205 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-55-8208          TCGA-55-8507          TCGA-55-8508 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-55-8511          TCGA-55-8512          TCGA-55-8619 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-55-8620          TCGA-55-A48Z          TCGA-55-A490 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-55-A494          TCGA-62-8394          TCGA-62-8395 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-62-8397          TCGA-62-8398          TCGA-62-8399 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-62-8402          TCGA-62-A46O          TCGA-62-A46P 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-62-A46R          TCGA-62-A46S          TCGA-62-A46U 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-62-A46V          TCGA-62-A46Y          TCGA-62-A470 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-62-A471          TCGA-62-A472          TCGA-64-1677 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-64-1681          TCGA-64-5778          TCGA-69-7974 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-69-8254          TCGA-71-6725          TCGA-71-8520 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-73-4659          TCGA-73-4662          TCGA-73-4666 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-73-4668          TCGA-73-4676          TCGA-73-7498 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-73-7499          TCGA-75-5122          TCGA-83-5908 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-86-7701          TCGA-86-7711          TCGA-86-7713 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-86-7714          TCGA-86-7954          TCGA-86-7955 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-86-8055          TCGA-86-8056          TCGA-86-8074 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-86-8075          TCGA-86-8076          TCGA-86-8278 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-86-8279          TCGA-86-8281          TCGA-86-8358 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-86-8359          TCGA-86-8668          TCGA-86-8669 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-86-8671          TCGA-86-A4JF          TCGA-86-A4P7 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-91-6849          TCGA-93-7348          TCGA-93-8067 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-93-A4JN          TCGA-93-A4JO          TCGA-MN-A4N1 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
         TCGA-MN-A4N4          TCGA-MN-A4N5 
"KRTAP5-10 WILD-TYPE" "KRTAP5-10 WILD-TYPE" 
                     vv
clus                  LUNG ACINAR ADENOCARCINOMA
  KRTAP5-10 MUTATED                            1
  KRTAP5-10 WILD-TYPE                         17
                     vv
clus                  LUNG ADENOCARCINOMA MIXED SUBTYPE
  KRTAP5-10 MUTATED                                   2
  KRTAP5-10 WILD-TYPE                               100
                     vv
clus                  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KRTAP5-10 MUTATED                                                    5
  KRTAP5-10 WILD-TYPE                                                289
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KRTAP5-10 MUTATED                                            0
  KRTAP5-10 WILD-TYPE                                          4
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KRTAP5-10 MUTATED                                               2
  KRTAP5-10 WILD-TYPE                                            17
                     vv
clus                  LUNG CLEAR CELL ADENOCARCINOMA
  KRTAP5-10 MUTATED                                0
  KRTAP5-10 WILD-TYPE                              2
                     vv
clus                  LUNG MICROPAPILLARY ADENOCARCINOMA
  KRTAP5-10 MUTATED                                    0
  KRTAP5-10 WILD-TYPE                                  3
                     vv
clus                  LUNG MUCINOUS ADENOCARCINOMA
  KRTAP5-10 MUTATED                              0
  KRTAP5-10 WILD-TYPE                            2
                     vv
clus                  LUNG PAPILLARY ADENOCARCINOMA
  KRTAP5-10 MUTATED                               0
  KRTAP5-10 WILD-TYPE                            22
                     vv
clus                  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KRTAP5-10 MUTATED                                               2
  KRTAP5-10 WILD-TYPE                                             3
                     vv
clus                  MUCINOUS (COLLOID) CARCINOMA
  KRTAP5-10 MUTATED                              0
  KRTAP5-10 WILD-TYPE                            9
D62V9, multiclass
                                                    clus
vv                                                   KRTAP5-10 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                         1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      2
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       0
  LUNG PAPILLARY ADENOCARCINOMA                                      0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       0
                                                    clus
vv                                                   KRTAP5-10 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                           4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                       17
  LUNG CLEAR CELL ADENOCARCINOMA                                       2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                   3
  LUNG MUCINOUS ADENOCARCINOMA                                         2
  LUNG PAPILLARY ADENOCARCINOMA                                       22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                        3
  MUCINOUS (COLLOID) CARCINOMA                                         9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED     0  12
  KRTAP5-10 WILD-TYPE  20 448
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      0   12
  KRTAP5-10 WILD-TYPE   20  448
     clus
vv    KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  NO                  0                  20
  YES                12                 448
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, continuous
                     vv
clus                   R0  R1  R2  RX
  KRTAP5-10 MUTATED     7   0   0   0
  KRTAP5-10 WILD-TYPE 303  11   4  25
D62V13, multiclass
    clus
vv   KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  R0                 7                 303
  R1                 0                  11
  R2                 0                   4
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP5-10 MUTATED                                  0     0
  KRTAP5-10 WILD-TYPE                                1     7
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-10 MUTATED                           1    10
  KRTAP5-10 WILD-TYPE                        28   367
D62V14, multiclass
                                  clus
vv                                 KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                   7
  BLACK OR AFRICAN AMERICAN                        1                  28
  WHITE                                           10                 367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED     1  10
  KRTAP5-10 WILD-TYPE   5 339
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      1   10
  KRTAP5-10 WILD-TYPE    5  339
                        clus
vv                       KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  HISPANIC OR LATINO                     1                   5
  NOT HISPANIC OR LATINO                10                 339
[1] 2 2
[1] FALSE

Clustering(63) Variable = PAK1 MUTATION ANALYSIS
D63V1, survival
                sevent
clus2              0   1
  PAK1 MUTATED     4   4
  PAK1 WILD-TYPE 311 137
  PAK1 MUTATED PAK1 WILD-TYPE 
             8            448 
  PAK1 MUTATED PAK1 WILD-TYPE 
             4            137 
$`PAK1 MUTATED`
TCGA-49-6744 TCGA-78-7150 TCGA-78-7156 TCGA-86-7713 TCGA-86-8672 TCGA-91-6830 
       29.26        21.90        32.09        13.87         0.62         1.97 
TCGA-95-7562 TCGA-97-7553 
        2.86        43.79 

$`PAK1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58        35.93        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        34.39        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       14.60         1.15        13.91        30.84        27.58        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        1.08        19.00        17.29         1.12         1.22        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
       18.18        19.89        31.69        64.60        63.52        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  PAK1 MUTATED PAK1 WILD-TYPE 
          0.62           0.00 
  PAK1 MUTATED PAK1 WILD-TYPE 
         43.79         223.96 
  PAK1 MUTATED PAK1 WILD-TYPE 
        17.885         18.030 
[1] "0.6 - 43.8 (17.9)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.2"
D63V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PAK1 MUTATED         0        2        0         4         2          0
  PAK1 WILD-TYPE       4      121      133        42        65         70
                vv
clus             STAGE IIIB STAGE IV
  PAK1 MUTATED            0        1
  PAK1 WILD-TYPE         11       24
D63V3, multiclass
            clus
vv           PAK1 MUTATED PAK1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              0            133
  STAGE IIA             4             42
  STAGE IIB             2             65
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK1 MUTATED     3   4   1   1
  PAK1 WILD-TYPE 152 257  42  17
D63V4, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  T1            3            152
  T2            4            257
  T3            1             42
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  PAK1 MUTATED     3   5     0
  PAK1 WILD-TYPE 304  84    72
D63V5, multiclass
       clus
vv      PAK1 MUTATED PAK1 WILD-TYPE
  N0               3            304
  N1               5             84
  N2+N3            0             72
[1] 3 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
  PAK1 MUTATED     5   1
  PAK1 WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      5    1
  PAK1 WILD-TYPE  322   22
   clus
vv  PAK1 MUTATED PAK1 WILD-TYPE
  0            5            322
  1            1             22
[1] 2 2
[1] FALSE
D63V7, binary
                cls
clus               0   1
  PAK1 MUTATED     3   6
  PAK1 WILD-TYPE 256 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      3    6
  PAK1 WILD-TYPE  256  215
        clus
vv       PAK1 MUTATED PAK1 WILD-TYPE
  FEMALE            3            256
  MALE              6            215
[1] 2 2
[1] FALSE
D63V8, continuous
[1] "Remove cluster labels:" "PAK1 MUTATED"          
clus
  PAK1 MUTATED PAK1 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7711 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8358     TCGA-86-8359 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PAK1 MUTATED                            0                                 2
  PAK1 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PAK1 MUTATED                                                    6
  PAK1 WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PAK1 MUTATED                                            0
  PAK1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PAK1 MUTATED                                               1
  PAK1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  PAK1 MUTATED                                0
  PAK1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  PAK1 MUTATED                                    0
  PAK1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PAK1 MUTATED                              0                             0
  PAK1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PAK1 MUTATED                                               0
  PAK1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  PAK1 MUTATED                              0
  PAK1 WILD-TYPE                            9
D63V9, multiclass
                                                    clus
vv                                                   PAK1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   PAK1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                cls
clus               0   1
  PAK1 MUTATED     0   9
  PAK1 WILD-TYPE  20 451
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      0    9
  PAK1 WILD-TYPE   20  451
     clus
vv    PAK1 MUTATED PAK1 WILD-TYPE
  NO             0             20
  YES            9            451
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, continuous
                vv
clus              R0  R1  R2  RX
  PAK1 MUTATED     5   0   0   1
  PAK1 WILD-TYPE 305  11   4  24
D63V13, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK1 MUTATED                                  0     0
  PAK1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK1 MUTATED                           1     8
  PAK1 WILD-TYPE                        28   369
D63V14, multiclass
                                  clus
vv                                 PAK1 MUTATED PAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, binary
                cls
clus               0   1
  PAK1 MUTATED     0   6
  PAK1 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      0    6
  PAK1 WILD-TYPE    6  343
                        clus
vv                       PAK1 MUTATED PAK1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(64) Variable = ABCC4 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  ABCC4 MUTATED    14   5
  ABCC4 WILD-TYPE 301 136
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             19             437 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              5             136 
$`ABCC4 MUTATED`
TCGA-05-4389 TCGA-05-4432 TCGA-44-3918 TCGA-44-8120 TCGA-49-4486 TCGA-50-5045 
       45.01        25.02        34.06         8.55        76.21        71.47 
TCGA-50-6673 TCGA-55-6968 TCGA-55-7995 TCGA-55-8207 TCGA-55-A4DG TCGA-67-3771 
        0.72        42.51         0.16         2.17        19.99        20.05 
TCGA-69-7765 TCGA-69-A59K TCGA-73-4670 TCGA-78-7146 TCGA-86-A4JF TCGA-95-7039 
        5.42         7.04         4.31         5.69        17.62         1.12 
TCGA-NJ-A55O 
        0.43 

$`ABCC4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
       29.00        17.59        23.64        12.66         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65         0.79        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15        19.82        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       13.87         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30        15.35         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       23.51       163.10        27.16        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26        19.82        59.11 

  ABCC4 MUTATED ABCC4 WILD-TYPE 
           0.16            0.00 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
          76.21          223.96 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
           8.55           18.12 
[1] "0.2 - 76.2 (8.6)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D64V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ABCC4 MUTATED         1        7        2         1         4          1
  ABCC4 WILD-TYPE       3      116      131        45        63         69
                 vv
clus              STAGE IIIB STAGE IV
  ABCC4 MUTATED            0        3
  ABCC4 WILD-TYPE         11       22
D64V3, multiclass
            clus
vv           ABCC4 MUTATED ABCC4 WILD-TYPE
  STAGE I                1               3
  STAGE IA               7             116
  STAGE IB               2             131
  STAGE IIA              1              45
  STAGE IIB              4              63
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               3              22
[1] 8 2
[1] TRUE
[1] "dimension of 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     9   6   3   1
  ABCC4 WILD-TYPE 146 255  40  17
D64V4, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  T1             9             146
  T2             6             255
  T3             3              40
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  ABCC4 MUTATED    15   3     1
  ABCC4 WILD-TYPE 292  86    71
D64V5, multiclass
       clus
vv      ABCC4 MUTATED ABCC4 WILD-TYPE
  N0               15             292
  N1                3              86
  N2+N3             1              71
[1] 3 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
  ABCC4 MUTATED    13   2
  ABCC4 WILD-TYPE 314  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     13    2
  ABCC4 WILD-TYPE  314   21
   clus
vv  ABCC4 MUTATED ABCC4 WILD-TYPE
  0            13             314
  1             2              21
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus                0   1
  ABCC4 MUTATED    10   9
  ABCC4 WILD-TYPE 249 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     10    9
  ABCC4 WILD-TYPE  249  212
        clus
vv       ABCC4 MUTATED ABCC4 WILD-TYPE
  FEMALE            10             249
  MALE               9             212
[1] 2 2
[1] FALSE
D64V8, continuous
[1] "Remove cluster labels:" "ABCC4 MUTATED"         
clus
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ABCC4 MUTATED                            1                                 6
  ABCC4 WILD-TYPE                         17                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ABCC4 MUTATED                                                   11
  ABCC4 WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ABCC4 MUTATED                                            0
  ABCC4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ABCC4 MUTATED                                               0
  ABCC4 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ABCC4 MUTATED                                0
  ABCC4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ABCC4 MUTATED                                    0
  ABCC4 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ABCC4 MUTATED                              0                             0
  ABCC4 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ABCC4 MUTATED                                               0
  ABCC4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ABCC4 MUTATED                              1
  ABCC4 WILD-TYPE                            8
D64V9, multiclass
                                                    clus
vv                                                   ABCC4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   ABCC4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, binary
                 cls
clus                0   1
  ABCC4 MUTATED     1  18
  ABCC4 WILD-TYPE  19 442
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED      1   18
  ABCC4 WILD-TYPE   19  442
     clus
vv    ABCC4 MUTATED ABCC4 WILD-TYPE
  NO              1              19
  YES            18             442
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, continuous
                 vv
clus               R0  R1  R2  RX
  ABCC4 MUTATED    12   0   0   0
  ABCC4 WILD-TYPE 298  11   4  25
D64V13, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  R0            12             298
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCC4 MUTATED                                  0     0
  ABCC4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCC4 MUTATED                           5    12
  ABCC4 WILD-TYPE                        24   365
D64V14, multiclass
                                  clus
vv                                 ABCC4 MUTATED ABCC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    5              24
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                 cls
clus                0   1
  ABCC4 MUTATED     0  15
  ABCC4 WILD-TYPE   6 334
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED      0   15
  ABCC4 WILD-TYPE    6  334
                        clus
vv                       ABCC4 MUTATED ABCC4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            15             334
[1] 2 2
[1] FALSE

Clustering(65) Variable = HERC4 MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2               0   1
  HERC4 MUTATED     9   4
  HERC4 WILD-TYPE 306 137
  HERC4 MUTATED HERC4 WILD-TYPE 
             13             443 
  HERC4 MUTATED HERC4 WILD-TYPE 
              4             137 
$`HERC4 MUTATED`
TCGA-05-4390 TCGA-05-4397 TCGA-44-6777 TCGA-50-5946 TCGA-55-1592 TCGA-55-8205 
       37.02        24.03        32.45        22.55        23.05         1.08 
TCGA-73-7499 TCGA-95-7567 TCGA-95-7948 TCGA-99-7458 TCGA-MN-A4N4 TCGA-MP-A4T4 
       23.51        18.67        15.65        24.56        38.63        86.04 
TCGA-NJ-A4YP 
        1.64 

$`HERC4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        63.72        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 
       27.25        34.29        30.54        13.94         9.21        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65        17.98         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        5.39         1.25        39.09       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
       19.00        17.29         1.12         1.22         2.86        12.39 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.68        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81         0.20        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  HERC4 MUTATED HERC4 WILD-TYPE 
           1.08            0.00 
  HERC4 MUTATED HERC4 WILD-TYPE 
          86.04          223.96 
  HERC4 MUTATED HERC4 WILD-TYPE 
          23.51           17.72 
[1] "1.1 - 86.0 (23.5)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "1.1"
D65V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HERC4 MUTATED         0        3        5         0         4          1
  HERC4 WILD-TYPE       4      120      128        46        63         69
                 vv
clus              STAGE IIIB STAGE IV
  HERC4 MUTATED            0        0
  HERC4 WILD-TYPE         11       25
D65V3, multiclass
            clus
vv           HERC4 MUTATED HERC4 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               5             128
  STAGE IIA              0              46
  STAGE IIB              4              63
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HERC4 MUTATED     2  10   0   1
  HERC4 WILD-TYPE 153 251  43  17
D65V4, multiclass
    clus
vv   HERC4 MUTATED HERC4 WILD-TYPE
  T1             2             153
  T2            10             251
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  HERC4 MUTATED     9   3     0
  HERC4 WILD-TYPE 298  86    72
D65V5, multiclass
       clus
vv      HERC4 MUTATED HERC4 WILD-TYPE
  N0                9             298
  N1                3              86
  N2+N3             0              72
[1] 3 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
  HERC4 MUTATED    11   0
  HERC4 WILD-TYPE 316  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC4 MUTATED     11    0
  HERC4 WILD-TYPE  316   23
   clus
vv  HERC4 MUTATED HERC4 WILD-TYPE
  0            11             316
  1             0              23
[1] 2 2
[1] FALSE
D65V7, binary
                 cls
clus                0   1
  HERC4 MUTATED     7   6
  HERC4 WILD-TYPE 252 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC4 MUTATED      7    6
  HERC4 WILD-TYPE  252  215
        clus
vv       HERC4 MUTATED HERC4 WILD-TYPE
  FEMALE             7             252
  MALE               6             215
[1] 2 2
[1] FALSE
D65V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HERC4 MUTATED                            0                                 6
  HERC4 WILD-TYPE                         18                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HERC4 MUTATED                                                    5
  HERC4 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HERC4 MUTATED                                            0
  HERC4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HERC4 MUTATED                                               1
  HERC4 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HERC4 MUTATED                                0
  HERC4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HERC4 MUTATED                                    0
  HERC4 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HERC4 MUTATED                              0                             1
  HERC4 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HERC4 MUTATED                                               0
  HERC4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HERC4 MUTATED                              0
  HERC4 WILD-TYPE                            9
D65V9, multiclass
                                                    clus
vv                                                   HERC4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HERC4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                 cls
clus                0   1
  HERC4 MUTATED     1  12
  HERC4 WILD-TYPE  19 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC4 MUTATED      1   12
  HERC4 WILD-TYPE   19  448
     clus
vv    HERC4 MUTATED HERC4 WILD-TYPE
  NO              1              19
  YES            12             448
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, continuous
                 vv
clus               R0  R1  R2  RX
  HERC4 MUTATED     9   0   0   0
  HERC4 WILD-TYPE 301  11   4  25
D65V13, multiclass
    clus
vv   HERC4 MUTATED HERC4 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HERC4 MUTATED                                  0     0
  HERC4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HERC4 MUTATED                           0    11
  HERC4 WILD-TYPE                        29   366
D65V14, multiclass
                                  clus
vv                                 HERC4 MUTATED HERC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, binary
                 cls
clus                0   1
  HERC4 MUTATED     0   8
  HERC4 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC4 MUTATED      0    8
  HERC4 WILD-TYPE    6  341
                        clus
vv                       HERC4 MUTATED HERC4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(66) Variable = DMRTB1 MUTATION ANALYSIS
D66V1, survival
                  sevent
clus2                0   1
  DMRTB1 MUTATED     6   3
  DMRTB1 WILD-TYPE 309 138
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               9              447 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               3              138 
$`DMRTB1 MUTATED`
TCGA-05-4382 TCGA-44-7662 TCGA-53-7626 TCGA-55-8506 TCGA-64-5775 TCGA-69-A59K 
       19.96         7.17        30.54         0.36         2.04         7.04 
TCGA-78-8662 TCGA-86-8054 TCGA-86-8073 
      110.50        24.49        24.33 

$`DMRTB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 
       61.28        16.44        14.60        19.46        12.03        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        34.29        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       20.65        55.43        38.37        87.98        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       14.01        13.45         4.24         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        16.70         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
            0.36             0.00 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
          110.50           223.96 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
           19.96            17.98 
[1] "0.4 - 110.5 (20.0)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D66V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DMRTB1 MUTATED         0        0        4         1         3          2
  DMRTB1 WILD-TYPE       4      123      129        45        64         68
                  vv
clus               STAGE IIIB STAGE IV
  DMRTB1 MUTATED            0        0
  DMRTB1 WILD-TYPE         11       25
D66V3, multiclass
            clus
vv           DMRTB1 MUTATED DMRTB1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0              123
  STAGE IB                4              129
  STAGE IIA               1               45
  STAGE IIB               3               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DMRTB1 MUTATED     1   6   2   1
  DMRTB1 WILD-TYPE 154 255  41  17
D66V4, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  T1              1              154
  T2              6              255
  T3              2               41
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  DMRTB1 MUTATED     7   2     1
  DMRTB1 WILD-TYPE 300  87    71
D66V5, multiclass
       clus
vv      DMRTB1 MUTATED DMRTB1 WILD-TYPE
  N0                 7              300
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  DMRTB1 MUTATED     8   0
  DMRTB1 WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      8    0
  DMRTB1 WILD-TYPE  319   23
   clus
vv  DMRTB1 MUTATED DMRTB1 WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D66V7, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   5
  DMRTB1 WILD-TYPE 254 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    5
  DMRTB1 WILD-TYPE  254  216
        clus
vv       DMRTB1 MUTATED DMRTB1 WILD-TYPE
  FEMALE              5              254
  MALE                5              216
[1] 2 2
[1] FALSE
D66V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DMRTB1 MUTATED                            1                                 2
  DMRTB1 WILD-TYPE                         17                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DMRTB1 MUTATED                                                    6
  DMRTB1 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DMRTB1 MUTATED                                            0
  DMRTB1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DMRTB1 MUTATED                                               1
  DMRTB1 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  DMRTB1 MUTATED                                0
  DMRTB1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  DMRTB1 MUTATED                                    0
  DMRTB1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DMRTB1 MUTATED                              0                             0
  DMRTB1 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DMRTB1 MUTATED                                               0
  DMRTB1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  DMRTB1 MUTATED                              0
  DMRTB1 WILD-TYPE                            9
D66V9, multiclass
                                                    clus
vv                                                   DMRTB1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   DMRTB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     0  10
  DMRTB1 WILD-TYPE  20 450
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      0   10
  DMRTB1 WILD-TYPE   20  450
     clus
vv    DMRTB1 MUTATED DMRTB1 WILD-TYPE
  NO               0               20
  YES             10              450
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, continuous
                  vv
clus                R0  R1  R2  RX
  DMRTB1 MUTATED     8   0   0   0
  DMRTB1 WILD-TYPE 302  11   4  25
D66V13, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  R0              8              302
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DMRTB1 MUTATED                                  0     0
  DMRTB1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DMRTB1 MUTATED                           1     6
  DMRTB1 WILD-TYPE                        28   371
D66V14, multiclass
                                  clus
vv                                 DMRTB1 MUTATED DMRTB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         6              371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     0   7
  DMRTB1 WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      0    7
  DMRTB1 WILD-TYPE    6  342
                        clus
vv                       DMRTB1 MUTATED DMRTB1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(67) Variable = C5AR1 MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  C5AR1 MUTATED     4   1
  C5AR1 WILD-TYPE 311 140
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              5             451 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              1             140 
$`C5AR1 MUTATED`
TCGA-05-4427 TCGA-05-5420 TCGA-73-4658 TCGA-86-8358 TCGA-97-7937 
       26.01        15.02        52.60        21.47         5.95 

$`C5AR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        7.04         2.01         0.10        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79        25.48         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  C5AR1 MUTATED C5AR1 WILD-TYPE 
           5.95            0.00 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
          52.60          223.96 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
          21.47           17.98 
[1] "6.0 - 52.6 (21.5)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D67V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C5AR1 MUTATED         0        0        3         0         1          1
  C5AR1 WILD-TYPE       4      123      130        46        66         69
                 vv
clus              STAGE IIIB STAGE IV
  C5AR1 MUTATED            0        0
  C5AR1 WILD-TYPE         11       25
D67V3, multiclass
            clus
vv           C5AR1 MUTATED C5AR1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  C5AR1 MUTATED     0   5   0   0
  C5AR1 WILD-TYPE 155 256  43  18
D67V4, multiclass
    clus
vv   C5AR1 MUTATED C5AR1 WILD-TYPE
  T1             0             155
  T2             5             256
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  C5AR1 MUTATED     3   1     1
  C5AR1 WILD-TYPE 304  88    71
D67V5, multiclass
       clus
vv      C5AR1 MUTATED C5AR1 WILD-TYPE
  N0                3             304
  N1                1              88
  N2+N3             1              71
[1] 3 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
  C5AR1 MUTATED     4   0
  C5AR1 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      4    0
  C5AR1 WILD-TYPE  323   23
   clus
vv  C5AR1 MUTATED C5AR1 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D67V7, binary
                 cls
clus                0   1
  C5AR1 MUTATED     2   3
  C5AR1 WILD-TYPE 257 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      2    3
  C5AR1 WILD-TYPE  257  218
        clus
vv       C5AR1 MUTATED C5AR1 WILD-TYPE
  FEMALE             2             257
  MALE               3             218
[1] 2 2
[1] FALSE
D67V8, continuous
[1] "Remove cluster labels:" "C5AR1 MUTATED"         
clus
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  C5AR1 MUTATED                            0                                 1
  C5AR1 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C5AR1 MUTATED                                                    3
  C5AR1 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C5AR1 MUTATED                                            0
  C5AR1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C5AR1 MUTATED                                               0
  C5AR1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  C5AR1 MUTATED                                0
  C5AR1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  C5AR1 MUTATED                                    1
  C5AR1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C5AR1 MUTATED                              0                             0
  C5AR1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C5AR1 MUTATED                                               0
  C5AR1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  C5AR1 MUTATED                              0
  C5AR1 WILD-TYPE                            9
D67V9, multiclass
                                                    clus
vv                                                   C5AR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   C5AR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                 cls
clus                0   1
  C5AR1 MUTATED     0   5
  C5AR1 WILD-TYPE  20 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      0    5
  C5AR1 WILD-TYPE   20  455
     clus
vv    C5AR1 MUTATED C5AR1 WILD-TYPE
  NO              0              20
  YES             5             455
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, continuous
                 vv
clus               R0  R1  R2  RX
  C5AR1 MUTATED     4   0   0   0
  C5AR1 WILD-TYPE 306  11   4  25
D67V13, multiclass
    clus
vv   C5AR1 MUTATED C5AR1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5AR1 MUTATED                                  0     0
  C5AR1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  C5AR1 MUTATED                           0     3
  C5AR1 WILD-TYPE                        29   374
D67V14, multiclass
                                  clus
vv                                 C5AR1 MUTATED C5AR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        3             374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, binary
                 cls
clus                0   1
  C5AR1 MUTATED     0   3
  C5AR1 WILD-TYPE   6 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      0    3
  C5AR1 WILD-TYPE    6  346
                        clus
vv                       C5AR1 MUTATED C5AR1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             346
[1] 2 2
[1] FALSE

Clustering(68) Variable = SLC26A10 MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  SLC26A10 MUTATED     9   5
  SLC26A10 WILD-TYPE 306 136
  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
                14                442 
  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
                 5                136 
$`SLC26A10 MUTATED`
TCGA-44-7670 TCGA-44-A479 TCGA-50-5045 TCGA-53-7624 TCGA-55-6972 TCGA-55-6985 
       29.00        15.98        71.47        34.29        48.49        40.54 
TCGA-69-7974 TCGA-69-7979 TCGA-78-7150 TCGA-86-8073 TCGA-86-8358 TCGA-97-7554 
        6.05         2.93        21.90        24.33        21.47        25.48 
TCGA-MP-A4TE TCGA-MP-A4TI 
       29.46        14.10 

$`SLC26A10 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
        2.20        45.34        32.71        60.03        24.99       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        7.56         2.30        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       20.58        35.93        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
       31.23         2.43        10.09        11.05        14.66        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
              2.93               0.00 
  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
             71.47             223.96 
  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
            24.905             17.735 
[1] "2.9 - 71.5 (24.9)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC26A10 MUTATED         0        1        6         3         1          2
  SLC26A10 WILD-TYPE       4      122      127        43        66         68
                    vv
clus                 STAGE IIIB STAGE IV
  SLC26A10 MUTATED            0        1
  SLC26A10 WILD-TYPE         11       24
D68V3, multiclass
            clus
vv           SLC26A10 MUTATED SLC26A10 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  1                122
  STAGE IB                  6                127
  STAGE IIA                 3                 43
  STAGE IIB                 1                 66
  STAGE IIIA                2                 68
  STAGE IIIB                0                 11
  STAGE IV                  1                 24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC26A10 MUTATED     1  13   0   0
  SLC26A10 WILD-TYPE 154 248  43  18
D68V4, multiclass
    clus
vv   SLC26A10 MUTATED SLC26A10 WILD-TYPE
  T1                1                154
  T2               13                248
  T3                0                 43
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  SLC26A10 MUTATED     8   4     2
  SLC26A10 WILD-TYPE 299  85    70
D68V5, multiclass
       clus
vv      SLC26A10 MUTATED SLC26A10 WILD-TYPE
  N0                   8                299
  N1                   4                 85
  N2+N3                2                 70
[1] 3 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
  SLC26A10 MUTATED     8   1
  SLC26A10 WILD-TYPE 319  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC26A10 MUTATED      8    1
  SLC26A10 WILD-TYPE  319   22
   clus
vv  SLC26A10 MUTATED SLC26A10 WILD-TYPE
  0                8                319
  1                1                 22
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  SLC26A10 MUTATED     8   6
  SLC26A10 WILD-TYPE 251 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC26A10 MUTATED      8    6
  SLC26A10 WILD-TYPE  251  215
        clus
vv       SLC26A10 MUTATED SLC26A10 WILD-TYPE
  FEMALE                8                251
  MALE                  6                215
[1] 2 2
[1] FALSE
D68V8, continuous
[1] "Remove cluster labels:" "SLC26A10 MUTATED"      
clus
  SLC26A10 MUTATED SLC26A10 WILD-TYPE 
                 2                 82 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-7283         TCGA-55-7573 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-55-7725         TCGA-55-7910         TCGA-55-7914 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8096         TCGA-55-8205 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8507         TCGA-55-8508 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8619 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-55-8620         TCGA-55-A48Z         TCGA-55-A490 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-55-A494         TCGA-62-8394         TCGA-62-8395 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-62-8397         TCGA-62-8398         TCGA-62-8399 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-62-8402         TCGA-62-A46O         TCGA-62-A46P 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-62-A46R         TCGA-62-A46S         TCGA-62-A46U 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-62-A46V         TCGA-62-A46Y         TCGA-62-A470 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-62-A471         TCGA-62-A472         TCGA-64-1677 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-64-1681         TCGA-64-5778         TCGA-69-8254 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-71-6725         TCGA-71-8520         TCGA-73-4659 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-73-4662         TCGA-73-4666         TCGA-73-4668 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-73-4676         TCGA-73-7498         TCGA-73-7499 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-75-5122         TCGA-83-5908         TCGA-86-7701 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-86-7711         TCGA-86-7713         TCGA-86-7714 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-86-7954         TCGA-86-7955         TCGA-86-8055 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-86-8056         TCGA-86-8074         TCGA-86-8075 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-86-8076         TCGA-86-8278         TCGA-86-8279 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-86-8281         TCGA-86-8359         TCGA-86-8668 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-86-8669         TCGA-86-8671         TCGA-86-A4JF 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-86-A4P7         TCGA-91-6849         TCGA-93-7348 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-93-8067         TCGA-93-A4JN         TCGA-93-A4JO 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-99-7458         TCGA-MN-A4N1         TCGA-MN-A4N4 
"SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" "SLC26A10 WILD-TYPE" 
        TCGA-MN-A4N5 
"SLC26A10 WILD-TYPE" 
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  SLC26A10 MUTATED                            1
  SLC26A10 WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC26A10 MUTATED                                   1
  SLC26A10 WILD-TYPE                               101
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC26A10 MUTATED                                                    9
  SLC26A10 WILD-TYPE                                                285
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC26A10 MUTATED                                            0
  SLC26A10 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC26A10 MUTATED                                               1
  SLC26A10 WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  SLC26A10 MUTATED                                0
  SLC26A10 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC26A10 MUTATED                                    0
  SLC26A10 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC26A10 MUTATED                              0                             2
  SLC26A10 WILD-TYPE                            2                            20
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC26A10 MUTATED                                               0
  SLC26A10 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  SLC26A10 MUTATED                              0
  SLC26A10 WILD-TYPE                            9
D68V9, multiclass
                                                    clus
vv                                                   SLC26A10 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   SLC26A10 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                    cls
clus                   0   1
  SLC26A10 MUTATED     2  12
  SLC26A10 WILD-TYPE  18 448
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC26A10 MUTATED      2   12
  SLC26A10 WILD-TYPE   18  448
     clus
vv    SLC26A10 MUTATED SLC26A10 WILD-TYPE
  NO                 2                 18
  YES               12                448
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, continuous
                    vv
clus                  R0  R1  R2  RX
  SLC26A10 MUTATED     9   0   0   1
  SLC26A10 WILD-TYPE 301  11   4  24
D68V13, multiclass
    clus
vv   SLC26A10 MUTATED SLC26A10 WILD-TYPE
  R0                9                301
  R1                0                 11
  R2                0                  4
  RX                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC26A10 MUTATED                                  0     0
  SLC26A10 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC26A10 MUTATED                           2    12
  SLC26A10 WILD-TYPE                        27   365
D68V14, multiclass
                                  clus
vv                                 SLC26A10 MUTATED SLC26A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       2                 27
  WHITE                                          12                365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                    cls
clus                   0   1
  SLC26A10 MUTATED     2  10
  SLC26A10 WILD-TYPE   4 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC26A10 MUTATED      2   10
  SLC26A10 WILD-TYPE    4  339
                        clus
vv                       SLC26A10 MUTATED SLC26A10 WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               10                339
[1] 2 2
[1] FALSE

Clustering(69) Variable = PTGIS MUTATION ANALYSIS
D69V1, survival
                 sevent
clus2               0   1
  PTGIS MUTATED     9   2
  PTGIS WILD-TYPE 306 139
  PTGIS MUTATED PTGIS WILD-TYPE 
             11             445 
  PTGIS MUTATED PTGIS WILD-TYPE 
              2             139 
$`PTGIS MUTATED`
TCGA-05-4398 TCGA-35-5375 TCGA-38-4625 TCGA-44-7670 TCGA-55-6972 TCGA-55-6975 
       47.05         8.68        97.74        29.00        48.49         3.88 
TCGA-55-7907 TCGA-55-8089 TCGA-55-A490 TCGA-69-7978 TCGA-MP-A4SY 
        0.53         3.29         1.58         2.30        49.35 

$`PTGIS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        2.04         7.40         5.98       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
       40.73        15.25         0.82         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 
        1.12         0.79         1.78         1.45        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       58.45        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PTGIS MUTATED PTGIS WILD-TYPE 
           0.53            0.00 
  PTGIS MUTATED PTGIS WILD-TYPE 
          97.74          223.96 
  PTGIS MUTATED PTGIS WILD-TYPE 
           8.68           18.08 
[1] "0.5 - 97.7 (8.7)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "2.2"
D69V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PTGIS MUTATED         0        1        2         3         3          1
  PTGIS WILD-TYPE       4      122      131        43        64         69
                 vv
clus              STAGE IIIB STAGE IV
  PTGIS MUTATED            1        0
  PTGIS WILD-TYPE         10       25
D69V3, multiclass
            clus
vv           PTGIS MUTATED PTGIS WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               2             131
  STAGE IIA              3              43
  STAGE IIB              3              64
  STAGE IIIA             1              69
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTGIS MUTATED     2   8   0   1
  PTGIS WILD-TYPE 153 253  43  17
D69V4, multiclass
    clus
vv   PTGIS MUTATED PTGIS WILD-TYPE
  T1             2             153
  T2             8             253
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  PTGIS MUTATED     4   5     2
  PTGIS WILD-TYPE 303  84    70
D69V5, multiclass
       clus
vv      PTGIS MUTATED PTGIS WILD-TYPE
  N0                4             303
  N1                5              84
  N2+N3             2              70
[1] 3 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
  PTGIS MUTATED     8   0
  PTGIS WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGIS MUTATED      8    0
  PTGIS WILD-TYPE  319   23
   clus
vv  PTGIS MUTATED PTGIS WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D69V7, binary
                 cls
clus                0   1
  PTGIS MUTATED     3   8
  PTGIS WILD-TYPE 256 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGIS MUTATED      3    8
  PTGIS WILD-TYPE  256  213
        clus
vv       PTGIS MUTATED PTGIS WILD-TYPE
  FEMALE             3             256
  MALE               8             213
[1] 2 2
[1] FALSE
D69V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PTGIS MUTATED                            0                                 3
  PTGIS WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTGIS MUTATED                                                    7
  PTGIS WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PTGIS MUTATED                                            0
  PTGIS WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PTGIS MUTATED                                               0
  PTGIS WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PTGIS MUTATED                                0
  PTGIS WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PTGIS MUTATED                                    0
  PTGIS WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PTGIS MUTATED                              0                             1
  PTGIS WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PTGIS MUTATED                                               0
  PTGIS WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PTGIS MUTATED                              0
  PTGIS WILD-TYPE                            9
D69V9, multiclass
                                                    clus
vv                                                   PTGIS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PTGIS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                 cls
clus                0   1
  PTGIS MUTATED     0  11
  PTGIS WILD-TYPE  20 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGIS MUTATED      0   11
  PTGIS WILD-TYPE   20  449
     clus
vv    PTGIS MUTATED PTGIS WILD-TYPE
  NO              0              20
  YES            11             449
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, continuous
                 vv
clus               R0  R1  R2  RX
  PTGIS MUTATED     8   0   0   0
  PTGIS WILD-TYPE 302  11   4  25
D69V13, multiclass
    clus
vv   PTGIS MUTATED PTGIS WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTGIS MUTATED                                  0     0
  PTGIS WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTGIS MUTATED                           0    10
  PTGIS WILD-TYPE                        29   367
D69V14, multiclass
                                  clus
vv                                 PTGIS MUTATED PTGIS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                 cls
clus                0   1
  PTGIS MUTATED     1   9
  PTGIS WILD-TYPE   5 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGIS MUTATED      1    9
  PTGIS WILD-TYPE    5  340
                        clus
vv                       PTGIS MUTATED PTGIS WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(70) Variable = DLX5 MUTATION ANALYSIS
D70V1, survival
                sevent
clus2              0   1
  DLX5 MUTATED     8   5
  DLX5 WILD-TYPE 307 136
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            443 
  DLX5 MUTATED DLX5 WILD-TYPE 
             5            136 
$`DLX5 MUTATED`
TCGA-38-4625 TCGA-50-6593 TCGA-55-8089 TCGA-55-8299 TCGA-55-8514 TCGA-86-6851 
       97.74        11.05         3.29        15.42         6.64         5.88 
TCGA-86-8054 TCGA-91-6828 TCGA-95-7043 TCGA-J2-A4AD TCGA-MP-A4T9 TCGA-MP-A4TA 
       24.49        10.62         1.22        18.08        41.59        31.23 
TCGA-NJ-A4YQ 
       29.13 

$`DLX5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        22.16         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       13.87        20.55        19.43        19.89        16.70         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       17.62        13.64        26.47        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        23.80        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        5.29         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64         0.26         0.43        19.82        59.11 

  DLX5 MUTATED DLX5 WILD-TYPE 
          1.22           0.00 
  DLX5 MUTATED DLX5 WILD-TYPE 
         97.74         223.96 
  DLX5 MUTATED DLX5 WILD-TYPE 
         15.42          18.12 
[1] "1.2 - 97.7 (15.4)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D70V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DLX5 MUTATED         0        7        2         1         1          2
  DLX5 WILD-TYPE       4      116      131        45        66         68
                vv
clus             STAGE IIIB STAGE IV
  DLX5 MUTATED            0        0
  DLX5 WILD-TYPE         11       25
D70V3, multiclass
            clus
vv           DLX5 MUTATED DLX5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              7            116
  STAGE IB              2            131
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DLX5 MUTATED     9   4   0   0
  DLX5 WILD-TYPE 146 257  43  18
D70V4, multiclass
    clus
vv   DLX5 MUTATED DLX5 WILD-TYPE
  T1            9            146
  T2            4            257
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  DLX5 MUTATED     9   2     2
  DLX5 WILD-TYPE 298  87    70
D70V5, multiclass
       clus
vv      DLX5 MUTATED DLX5 WILD-TYPE
  N0               9            298
  N1               2             87
  N2+N3            2             70
[1] 3 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
  DLX5 MUTATED     8   0
  DLX5 WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED      8    0
  DLX5 WILD-TYPE  319   23
   clus
vv  DLX5 MUTATED DLX5 WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D70V7, binary
                cls
clus               0   1
  DLX5 MUTATED    10   3
  DLX5 WILD-TYPE 249 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED     10    3
  DLX5 WILD-TYPE  249  218
        clus
vv       DLX5 MUTATED DLX5 WILD-TYPE
  FEMALE           10            249
  MALE              3            218
[1] 2 2
[1] FALSE
D70V8, continuous
[1] "Remove cluster labels:" "DLX5 MUTATED"          
clus
  DLX5 MUTATED DLX5 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"DLX5 WILD-TYPE" "DLX5 WILD-TYPE" "DLX5 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DLX5 MUTATED                            1                                 3
  DLX5 WILD-TYPE                         17                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DLX5 MUTATED                                                    9
  DLX5 WILD-TYPE                                                285
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DLX5 MUTATED                                            0
  DLX5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DLX5 MUTATED                                               0
  DLX5 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  DLX5 MUTATED                                0
  DLX5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  DLX5 MUTATED                                    0
  DLX5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DLX5 MUTATED                              0                             0
  DLX5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DLX5 MUTATED                                               0
  DLX5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  DLX5 MUTATED                              0
  DLX5 WILD-TYPE                            9
D70V9, multiclass
                                                    clus
vv                                                   DLX5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   DLX5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                cls
clus               0   1
  DLX5 MUTATED     0  13
  DLX5 WILD-TYPE  20 447
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED      0   13
  DLX5 WILD-TYPE   20  447
     clus
vv    DLX5 MUTATED DLX5 WILD-TYPE
  NO             0             20
  YES           13            447
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, continuous
                vv
clus              R0  R1  R2  RX
  DLX5 MUTATED     8   0   0   3
  DLX5 WILD-TYPE 302  11   4  22
D70V13, multiclass
    clus
vv   DLX5 MUTATED DLX5 WILD-TYPE
  R0            8            302
  R1            0             11
  R2            0              4
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLX5 MUTATED                                  0     0
  DLX5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DLX5 MUTATED                           1    12
  DLX5 WILD-TYPE                        28   365
D70V14, multiclass
                                  clus
vv                                 DLX5 MUTATED DLX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      12            365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
                cls
clus               0   1
  DLX5 MUTATED     0  13
  DLX5 WILD-TYPE   6 336
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED      0   13
  DLX5 WILD-TYPE    6  336
                        clus
vv                       DLX5 MUTATED DLX5 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           13            336
[1] 2 2
[1] FALSE

Clustering(71) Variable = GPATCH4 MUTATION ANALYSIS
D71V1, survival
                   sevent
clus2                 0   1
  GPATCH4 MUTATED     4   4
  GPATCH4 WILD-TYPE 311 137
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                8               448 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                4               137 
$`GPATCH4 MUTATED`
TCGA-05-4398 TCGA-50-6592 TCGA-55-7284 TCGA-55-8092 TCGA-55-A4DF TCGA-86-8585 
       47.05        25.55         7.99         5.06        20.19         1.15 
TCGA-91-6848 TCGA-95-7039 
        7.36         1.12 

$`GPATCH4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         1.15         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
        1.58        20.58        19.59         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
             1.12              0.00 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            47.05            223.96 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            7.675            18.100 
[1] "1.1 - 47.0 (7.7)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "2.8"
D71V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GPATCH4 MUTATED         0        1        2         0         3          1
  GPATCH4 WILD-TYPE       4      122      131        46        64         69
                   vv
clus                STAGE IIIB STAGE IV
  GPATCH4 MUTATED            1        0
  GPATCH4 WILD-TYPE         10       25
D71V3, multiclass
            clus
vv           GPATCH4 MUTATED GPATCH4 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 2               131
  STAGE IIA                0                46
  STAGE IIB                3                64
  STAGE IIIA               1                69
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of 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     1   3   3   1
  GPATCH4 WILD-TYPE 154 258  40  17
D71V4, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  T1               1               154
  T2               3               258
  T3               3                40
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  GPATCH4 MUTATED     6   0     2
  GPATCH4 WILD-TYPE 301  89    70
D71V5, multiclass
       clus
vv      GPATCH4 MUTATED GPATCH4 WILD-TYPE
  N0                  6               301
  N1                  0                89
  N2+N3               2                70
[1] 3 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
  GPATCH4 MUTATED     3   0
  GPATCH4 WILD-TYPE 324  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      3    0
  GPATCH4 WILD-TYPE  324   23
   clus
vv  GPATCH4 MUTATED GPATCH4 WILD-TYPE
  0               3               324
  1               0                23
[1] 2 2
[1] FALSE
D71V7, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     3   5
  GPATCH4 WILD-TYPE 256 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      3    5
  GPATCH4 WILD-TYPE  256  216
        clus
vv       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  FEMALE               3               256
  MALE                 5               216
[1] 2 2
[1] FALSE
D71V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  GPATCH4 MUTATED                            0
  GPATCH4 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  GPATCH4 MUTATED                                   2
  GPATCH4 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GPATCH4 MUTATED                                                    4
  GPATCH4 WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GPATCH4 MUTATED                                            0
  GPATCH4 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GPATCH4 MUTATED                                               1
  GPATCH4 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  GPATCH4 MUTATED                                0
  GPATCH4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  GPATCH4 MUTATED                                    0
  GPATCH4 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GPATCH4 MUTATED                              0                             0
  GPATCH4 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GPATCH4 MUTATED                                               1
  GPATCH4 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  GPATCH4 MUTATED                              0
  GPATCH4 WILD-TYPE                            9
D71V9, multiclass
                                                    clus
vv                                                   GPATCH4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   GPATCH4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     0   8
  GPATCH4 WILD-TYPE  20 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      0    8
  GPATCH4 WILD-TYPE   20  452
     clus
vv    GPATCH4 MUTATED GPATCH4 WILD-TYPE
  NO                0                20
  YES               8               452
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, continuous
[1] "Remove cluster labels:" "GPATCH4 MUTATED"       
clus
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                1               256 
       TCGA-05-4384        TCGA-05-4390        TCGA-05-4396        TCGA-05-4405 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-05-4410        TCGA-05-4415        TCGA-05-4417        TCGA-05-4424 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-05-4427        TCGA-05-4433        TCGA-05-5420        TCGA-05-5423 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5428        TCGA-35-4122        TCGA-35-4123 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-35-5375        TCGA-38-4625        TCGA-38-4626        TCGA-38-7271 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-38-A44F        TCGA-44-2656        TCGA-44-2657        TCGA-44-3396 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-3398        TCGA-44-3918        TCGA-44-4112        TCGA-44-5644 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6147 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-6148        TCGA-44-6774        TCGA-44-6775        TCGA-44-6776 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-6777        TCGA-44-6778        TCGA-44-6779        TCGA-44-7659 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-7660        TCGA-44-7661        TCGA-44-7662        TCGA-44-7667 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-7669        TCGA-44-7670        TCGA-44-7672        TCGA-44-8117 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-8119        TCGA-44-8120        TCGA-44-A479        TCGA-44-A47A 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-A47B        TCGA-44-A47F        TCGA-44-A47G        TCGA-44-A4SS 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-44-A4SU        TCGA-49-4486        TCGA-49-4494        TCGA-49-4505 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-53-A4EZ 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-1592        TCGA-55-1595        TCGA-55-5899        TCGA-55-6642 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-6712        TCGA-55-6971        TCGA-55-7227        TCGA-55-7283 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-7570        TCGA-55-7574        TCGA-55-7576        TCGA-55-7724 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-7725        TCGA-55-7726        TCGA-55-7728        TCGA-55-7907 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7911        TCGA-55-7914        TCGA-55-8089 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-8094        TCGA-55-8096        TCGA-55-8097        TCGA-55-8205 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-8299        TCGA-55-8301        TCGA-55-8302        TCGA-55-8506 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8511        TCGA-55-8512        TCGA-55-8514 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-8615        TCGA-55-8620        TCGA-55-8621        TCGA-55-A48X 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-A48Y        TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A491 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-55-A492        TCGA-55-A493        TCGA-55-A494        TCGA-62-8398 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1681        TCGA-64-5774        TCGA-64-5775 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-64-5778        TCGA-64-5779        TCGA-64-5781        TCGA-69-7761 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-69-7763        TCGA-69-7764        TCGA-69-7765        TCGA-69-7974 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-69-7979        TCGA-69-8253        TCGA-69-8255        TCGA-69-A59K 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7025        TCGA-75-7027        TCGA-75-7031 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-7145        TCGA-78-7146        TCGA-78-7147        TCGA-78-7148 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-7149        TCGA-78-7150        TCGA-78-7152        TCGA-78-7153 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-7154        TCGA-78-7155        TCGA-78-7156        TCGA-78-7158 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-7159        TCGA-78-7160        TCGA-78-7161        TCGA-78-7162 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-7163        TCGA-78-7166        TCGA-78-7167        TCGA-78-7220 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-7542        TCGA-78-7633        TCGA-78-8640        TCGA-78-8648 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-78-8655        TCGA-78-8660        TCGA-78-8662        TCGA-80-5607 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-80-5608        TCGA-83-5908        TCGA-86-6851        TCGA-86-7711 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-8054        TCGA-86-8055 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8073        TCGA-86-8074        TCGA-86-8281 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8669        TCGA-86-8673 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-86-8674        TCGA-86-A456        TCGA-91-6829        TCGA-91-6830 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6849        TCGA-91-8499 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-91-A4BC        TCGA-93-7347        TCGA-93-7348        TCGA-93-8067 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-93-A4JQ        TCGA-95-7043 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-95-7562        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-95-7948        TCGA-95-A4VK        TCGA-95-A4VN        TCGA-95-A4VP 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-97-7546        TCGA-97-7553        TCGA-97-7554        TCGA-97-7941 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-97-8171        TCGA-97-8172        TCGA-97-8174        TCGA-97-8176 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-97-8179        TCGA-97-A4LX        TCGA-97-A4M0        TCGA-97-A4M1 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-97-A4M2        TCGA-97-A4M3        TCGA-97-A4M5        TCGA-97-A4M7 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-99-7458        TCGA-99-8025        TCGA-99-8028        TCGA-99-8032 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-J2-8194        TCGA-J2-A4AD        TCGA-J2-A4AG        TCGA-L4-A4E5 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L4-A4E6        TCGA-L9-A443        TCGA-L9-A444        TCGA-MN-A4N1 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5        TCGA-MP-A4SV        TCGA-MP-A4SW 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-MP-A4T2        TCGA-MP-A4T4        TCGA-MP-A4T7        TCGA-MP-A4T8 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-MP-A4T9        TCGA-MP-A4TA        TCGA-MP-A4TC        TCGA-MP-A4TE 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-MP-A4TF        TCGA-MP-A4TH        TCGA-MP-A4TI        TCGA-MP-A4TK 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-MP-A5C7        TCGA-NJ-A4YG        TCGA-NJ-A4YI        TCGA-O1-A52J 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  GPATCH4 MUTATED     5   0   0   0
  GPATCH4 WILD-TYPE 305  11   4  25
D71V13, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  R0               5               305
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPATCH4 MUTATED                                  0     0
  GPATCH4 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GPATCH4 MUTATED                           0     7
  GPATCH4 WILD-TYPE                        29   370
D71V14, multiclass
                                  clus
vv                                 GPATCH4 MUTATED GPATCH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          7               370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     0   7
  GPATCH4 WILD-TYPE   6 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      0    7
  GPATCH4 WILD-TYPE    6  342
                        clus
vv                       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               7               342
[1] 2 2
[1] FALSE

Clustering(72) Variable = NR4A2 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  NR4A2 MUTATED    15   2
  NR4A2 WILD-TYPE 300 139
  NR4A2 MUTATED NR4A2 WILD-TYPE 
             17             439 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
              2             139 
$`NR4A2 MUTATED`
TCGA-35-5375 TCGA-44-3398 TCGA-44-7670 TCGA-44-8117 TCGA-44-A479 TCGA-50-6590 
        8.68        38.24        29.00        12.66        15.98        42.35 
TCGA-50-6594 TCGA-55-7281 TCGA-55-7903 TCGA-55-8208 TCGA-64-5781 TCGA-86-8279 
       12.16         0.59        18.64        22.16        51.25        15.85 
TCGA-86-8585 TCGA-86-A4JF TCGA-97-7937 TCGA-99-8028 TCGA-NJ-A4YP 
        1.15        17.62         5.95        36.76         1.64 

$`NR4A2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         5.98        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A 
       18.87        17.59        23.64         3.25         8.55        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        11.05         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1.74         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78         1.45         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       16.08        15.65        23.05        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        34.85         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  NR4A2 MUTATED NR4A2 WILD-TYPE 
           0.59            0.00 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
          51.25          223.96 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
          15.98           18.12 
[1] "0.6 - 51.2 (16.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.2"
D72V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NR4A2 MUTATED         0        5        7         2         1          2
  NR4A2 WILD-TYPE       4      118      126        44        66         68
                 vv
clus              STAGE IIIB STAGE IV
  NR4A2 MUTATED            0        0
  NR4A2 WILD-TYPE         11       25
D72V3, multiclass
            clus
vv           NR4A2 MUTATED NR4A2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               7             126
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NR4A2 MUTATED     6   9   2   0
  NR4A2 WILD-TYPE 149 252  41  18
D72V4, multiclass
    clus
vv   NR4A2 MUTATED NR4A2 WILD-TYPE
  T1             6             149
  T2             9             252
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  NR4A2 MUTATED    13   2     2
  NR4A2 WILD-TYPE 294  87    70
D72V5, multiclass
       clus
vv      NR4A2 MUTATED NR4A2 WILD-TYPE
  N0               13             294
  N1                2              87
  N2+N3             2              70
[1] 3 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
  NR4A2 MUTATED    14   0
  NR4A2 WILD-TYPE 313  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED     14    0
  NR4A2 WILD-TYPE  313   23
   clus
vv  NR4A2 MUTATED NR4A2 WILD-TYPE
  0            14             313
  1             0              23
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus                0   1
  NR4A2 MUTATED    10   7
  NR4A2 WILD-TYPE 249 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED     10    7
  NR4A2 WILD-TYPE  249  214
        clus
vv       NR4A2 MUTATED NR4A2 WILD-TYPE
  FEMALE            10             249
  MALE               7             214
[1] 2 2
[1] FALSE
D72V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NR4A2 MUTATED                            0                                 1
  NR4A2 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NR4A2 MUTATED                                                   13
  NR4A2 WILD-TYPE                                                281
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NR4A2 MUTATED                                            0
  NR4A2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NR4A2 MUTATED                                               0
  NR4A2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NR4A2 MUTATED                                0
  NR4A2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NR4A2 MUTATED                                    1
  NR4A2 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NR4A2 MUTATED                              0                             1
  NR4A2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NR4A2 MUTATED                                               1
  NR4A2 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NR4A2 MUTATED                              0
  NR4A2 WILD-TYPE                            9
D72V9, multiclass
                                                    clus
vv                                                   NR4A2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NR4A2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                 cls
clus                0   1
  NR4A2 MUTATED     0  17
  NR4A2 WILD-TYPE  20 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      0   17
  NR4A2 WILD-TYPE   20  443
     clus
vv    NR4A2 MUTATED NR4A2 WILD-TYPE
  NO              0              20
  YES            17             443
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, continuous
                 vv
clus               R0  R1  R2  RX
  NR4A2 MUTATED    11   0   0   0
  NR4A2 WILD-TYPE 299  11   4  25
D72V13, multiclass
    clus
vv   NR4A2 MUTATED NR4A2 WILD-TYPE
  R0            11             299
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NR4A2 MUTATED                                  0     0
  NR4A2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NR4A2 MUTATED                           3    14
  NR4A2 WILD-TYPE                        26   363
D72V14, multiclass
                                  clus
vv                                 NR4A2 MUTATED NR4A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              26
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                 cls
clus                0   1
  NR4A2 MUTATED     1  15
  NR4A2 WILD-TYPE   5 334
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      1   15
  NR4A2 WILD-TYPE    5  334
                        clus
vv                       NR4A2 MUTATED NR4A2 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            15             334
[1] 2 2
[1] FALSE

Clustering(73) Variable = ABHD12B MUTATION ANALYSIS
D73V1, survival
                   sevent
clus2                 0   1
  ABHD12B MUTATED     3   4
  ABHD12B WILD-TYPE 312 137
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               449 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                4               137 
$`ABHD12B MUTATED`
TCGA-44-6779 TCGA-49-4501 TCGA-55-6968 TCGA-55-7994 TCGA-78-7147 TCGA-99-8032 
       16.44        46.72        42.51        19.82        19.27         1.45 
TCGA-NJ-A4YP 
        1.64 

$`ABHD12B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       32.45        61.28        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85        36.76         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ABHD12B MUTATED ABHD12B WILD-TYPE 
             1.45              0.00 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
            46.72            223.96 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
            19.27             17.98 
[1] "1.4 - 46.7 (19.3)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2"  
D73V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ABHD12B MUTATED         0        1        2         0         3          0
  ABHD12B WILD-TYPE       4      122      131        46        64         70
                   vv
clus                STAGE IIIB STAGE IV
  ABHD12B MUTATED            0        1
  ABHD12B WILD-TYPE         11       24
D73V3, multiclass
            clus
vv           ABHD12B MUTATED ABHD12B WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 2               131
  STAGE IIA                0                46
  STAGE IIB                3                64
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ABHD12B MUTATED     2   4   1   0
  ABHD12B WILD-TYPE 153 257  42  18
D73V4, multiclass
    clus
vv   ABHD12B MUTATED ABHD12B WILD-TYPE
  T1               2               153
  T2               4               257
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  ABHD12B MUTATED     5   2     0
  ABHD12B WILD-TYPE 302  87    72
D73V5, multiclass
       clus
vv      ABHD12B MUTATED ABHD12B WILD-TYPE
  N0                  5               302
  N1                  2                87
  N2+N3               0                72
[1] 3 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
  ABHD12B MUTATED     4   1
  ABHD12B WILD-TYPE 323  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      4    1
  ABHD12B WILD-TYPE  323   22
   clus
vv  ABHD12B MUTATED ABHD12B WILD-TYPE
  0               4               323
  1               1                22
[1] 2 2
[1] FALSE
D73V7, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     3   4
  ABHD12B WILD-TYPE 256 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      3    4
  ABHD12B WILD-TYPE  256  217
        clus
vv       ABHD12B MUTATED ABHD12B WILD-TYPE
  FEMALE               3               256
  MALE                 4               217
[1] 2 2
[1] FALSE
D73V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ABHD12B MUTATED                            0
  ABHD12B WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ABHD12B MUTATED                                   0
  ABHD12B WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ABHD12B MUTATED                                                    6
  ABHD12B WILD-TYPE                                                288
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ABHD12B MUTATED                                            0
  ABHD12B WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ABHD12B MUTATED                                               0
  ABHD12B WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ABHD12B MUTATED                                0
  ABHD12B WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ABHD12B MUTATED                                    0
  ABHD12B WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ABHD12B MUTATED                              0                             1
  ABHD12B WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ABHD12B MUTATED                                               0
  ABHD12B WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ABHD12B MUTATED                              0
  ABHD12B WILD-TYPE                            9
D73V9, multiclass
                                                    clus
vv                                                   ABHD12B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ABHD12B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     0   7
  ABHD12B WILD-TYPE  20 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      0    7
  ABHD12B WILD-TYPE   20  453
     clus
vv    ABHD12B MUTATED ABHD12B WILD-TYPE
  NO                0                20
  YES               7               453
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ABHD12B MUTATED     4   0   0   0
  ABHD12B WILD-TYPE 306  11   4  25
D73V13, multiclass
    clus
vv   ABHD12B MUTATED ABHD12B WILD-TYPE
  R0               4               306
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABHD12B MUTATED                                  0     0
  ABHD12B WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ABHD12B MUTATED                           0     7
  ABHD12B WILD-TYPE                        29   370
D73V14, multiclass
                                  clus
vv                                 ABHD12B MUTATED ABHD12B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          7               370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     0   5
  ABHD12B WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      0    5
  ABHD12B WILD-TYPE    6  344
                        clus
vv                       ABHD12B MUTATED ABHD12B WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(74) Variable = FNDC7 MUTATION ANALYSIS
D74V1, survival
                 sevent
clus2               0   1
  FNDC7 MUTATED     8   2
  FNDC7 WILD-TYPE 307 139
  FNDC7 MUTATED FNDC7 WILD-TYPE 
             10             446 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              2             139 
$`FNDC7 MUTATED`
TCGA-05-4382 TCGA-44-3918 TCGA-55-8090 TCGA-55-8513 TCGA-55-A492 TCGA-73-4677 
       19.96        34.06        19.66         4.80        19.59         1.25 
TCGA-86-8279 TCGA-86-8674 TCGA-86-A4JF TCGA-97-7937 
       15.85        13.32        17.62         5.95 

$`FNDC7 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.30         0.10         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        20.58         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        1.32         5.39        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.65        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 
       30.84        27.58         0.62        14.96        13.32        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  FNDC7 MUTATED FNDC7 WILD-TYPE 
           1.25            0.00 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
          34.06          223.96 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
         16.735          18.100 
[1] "1.2 - 34.1 (16.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D74V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FNDC7 MUTATED         0        4        2         2         2          0
  FNDC7 WILD-TYPE       4      119      131        44        65         70
                 vv
clus              STAGE IIIB STAGE IV
  FNDC7 MUTATED            0        0
  FNDC7 WILD-TYPE         11       25
D74V3, multiclass
            clus
vv           FNDC7 MUTATED FNDC7 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               2             131
  STAGE IIA              2              44
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FNDC7 MUTATED     3   5   2   0
  FNDC7 WILD-TYPE 152 256  41  18
D74V4, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  T1             3             152
  T2             5             256
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  FNDC7 MUTATED     8   2     0
  FNDC7 WILD-TYPE 299  87    72
D74V5, multiclass
       clus
vv      FNDC7 MUTATED FNDC7 WILD-TYPE
  N0                8             299
  N1                2              87
  N2+N3             0              72
[1] 3 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
  FNDC7 MUTATED     7   0
  FNDC7 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      7    0
  FNDC7 WILD-TYPE  320   23
   clus
vv  FNDC7 MUTATED FNDC7 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D74V7, binary
                 cls
clus                0   1
  FNDC7 MUTATED     3   7
  FNDC7 WILD-TYPE 256 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      3    7
  FNDC7 WILD-TYPE  256  214
        clus
vv       FNDC7 MUTATED FNDC7 WILD-TYPE
  FEMALE             3             256
  MALE               7             214
[1] 2 2
[1] FALSE
D74V8, continuous
[1] "Remove cluster labels:" "FNDC7 MUTATED"         
clus
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8281      TCGA-86-8358 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FNDC7 MUTATED                            0                                 1
  FNDC7 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FNDC7 MUTATED                                                    6
  FNDC7 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FNDC7 MUTATED                                            0
  FNDC7 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FNDC7 MUTATED                                               0
  FNDC7 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FNDC7 MUTATED                                0
  FNDC7 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FNDC7 MUTATED                                    1
  FNDC7 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FNDC7 MUTATED                              0                             1
  FNDC7 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FNDC7 MUTATED                                               0
  FNDC7 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FNDC7 MUTATED                              1
  FNDC7 WILD-TYPE                            8
D74V9, multiclass
                                                    clus
vv                                                   FNDC7 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   FNDC7 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                 cls
clus                0   1
  FNDC7 MUTATED     0  10
  FNDC7 WILD-TYPE  20 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      0   10
  FNDC7 WILD-TYPE   20  450
     clus
vv    FNDC7 MUTATED FNDC7 WILD-TYPE
  NO              0              20
  YES            10             450
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, continuous
                 vv
clus               R0  R1  R2  RX
  FNDC7 MUTATED     9   0   0   0
  FNDC7 WILD-TYPE 301  11   4  25
D74V13, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FNDC7 MUTATED                                  0     0
  FNDC7 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FNDC7 MUTATED                           0     9
  FNDC7 WILD-TYPE                        29   368
D74V14, multiclass
                                  clus
vv                                 FNDC7 MUTATED FNDC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                 cls
clus                0   1
  FNDC7 MUTATED     0   9
  FNDC7 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      0    9
  FNDC7 WILD-TYPE    6  340
                        clus
vv                       FNDC7 MUTATED FNDC7 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(75) Variable = RIT1 MUTATION ANALYSIS
D75V1, survival
                sevent
clus2              0   1
  RIT1 MUTATED     7   1
  RIT1 WILD-TYPE 308 140
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            448 
  RIT1 MUTATED RIT1 WILD-TYPE 
             1            140 
$`RIT1 MUTATED`
TCGA-05-4384 TCGA-44-6779 TCGA-49-4514 TCGA-55-8094 TCGA-73-4666 TCGA-73-4675 
       14.01        16.44        55.89         0.13        26.30         1.32 
TCGA-86-A4JF TCGA-J2-A4AE 
       17.62        35.47 

$`RIT1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        23.38        29.98        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG 
        1.45         5.59        24.30        23.80        18.08        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  RIT1 MUTATED RIT1 WILD-TYPE 
          0.13           0.00 
  RIT1 MUTATED RIT1 WILD-TYPE 
         55.89         223.96 
  RIT1 MUTATED RIT1 WILD-TYPE 
         17.03          18.10 
[1] "0.1 - 55.9 (17.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.3"
D75V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RIT1 MUTATED         0        2        0         0         2          2
  RIT1 WILD-TYPE       4      121      133        46        65         68
                vv
clus             STAGE IIIB STAGE IV
  RIT1 MUTATED            0        2
  RIT1 WILD-TYPE         11       23
D75V3, multiclass
            clus
vv           RIT1 MUTATED RIT1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              0            133
  STAGE IIA             0             46
  STAGE IIB             2             65
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RIT1 MUTATED     3   3   2   0
  RIT1 WILD-TYPE 152 258  41  18
D75V4, multiclass
    clus
vv   RIT1 MUTATED RIT1 WILD-TYPE
  T1            3            152
  T2            3            258
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  RIT1 MUTATED     5   2     1
  RIT1 WILD-TYPE 302  87    71
D75V5, multiclass
       clus
vv      RIT1 MUTATED RIT1 WILD-TYPE
  N0               5            302
  N1               2             87
  N2+N3            1             71
[1] 3 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
  RIT1 MUTATED     4   2
  RIT1 WILD-TYPE 323  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      4    2
  RIT1 WILD-TYPE  323   21
   clus
vv  RIT1 MUTATED RIT1 WILD-TYPE
  0            4            323
  1            2             21
[1] 2 2
[1] FALSE
D75V7, binary
                cls
clus               0   1
  RIT1 MUTATED     4   4
  RIT1 WILD-TYPE 255 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      4    4
  RIT1 WILD-TYPE  255  217
        clus
vv       RIT1 MUTATED RIT1 WILD-TYPE
  FEMALE            4            255
  MALE              4            217
[1] 2 2
[1] FALSE
D75V8, continuous
[1] "Remove cluster labels:" "RIT1 MUTATED"          
clus
  RIT1 MUTATED RIT1 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4668 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RIT1 MUTATED                            0                                 1
  RIT1 WILD-TYPE                         18                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RIT1 MUTATED                                                    6
  RIT1 WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RIT1 MUTATED                                            0
  RIT1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RIT1 MUTATED                                               0
  RIT1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RIT1 MUTATED                                0
  RIT1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RIT1 MUTATED                                    0
  RIT1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RIT1 MUTATED                              0                             1
  RIT1 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RIT1 MUTATED                                               0
  RIT1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RIT1 MUTATED                              0
  RIT1 WILD-TYPE                            9
D75V9, multiclass
                                                    clus
vv                                                   RIT1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RIT1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, binary
                cls
clus               0   1
  RIT1 MUTATED     1   7
  RIT1 WILD-TYPE  19 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      1    7
  RIT1 WILD-TYPE   19  453
     clus
vv    RIT1 MUTATED RIT1 WILD-TYPE
  NO             1             19
  YES            7            453
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, continuous
                vv
clus              R0  R1  R2  RX
  RIT1 MUTATED     5   0   0   2
  RIT1 WILD-TYPE 305  11   4  23
D75V13, multiclass
    clus
vv   RIT1 MUTATED RIT1 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIT1 MUTATED                                  0     0
  RIT1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RIT1 MUTATED                           0     7
  RIT1 WILD-TYPE                        29   370
D75V14, multiclass
                                  clus
vv                                 RIT1 MUTATED RIT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                cls
clus               0   1
  RIT1 MUTATED     0   5
  RIT1 WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      0    5
  RIT1 WILD-TYPE    6  344
                        clus
vv                       RIT1 MUTATED RIT1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(76) Variable = ASCL3 MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2               0   1
  ASCL3 MUTATED     5   2
  ASCL3 WILD-TYPE 310 139
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             449 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              2             139 
$`ASCL3 MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-50-5939 TCGA-55-8094 TCGA-55-A4DG TCGA-86-A4JF 
       19.96         8.02        15.12         0.13        19.99        17.62 
TCGA-95-7039 
        1.12 

$`ASCL3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 
       40.60        78.67        21.47         8.45        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ASCL3 MUTATED ASCL3 WILD-TYPE 
           0.13            0.00 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
          19.99          223.96 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
          15.12           18.12 
[1] "0.1 - 20.0 (15.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.3"
D76V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ASCL3 MUTATED         0        1        2         0         2          0
  ASCL3 WILD-TYPE       4      122      131        46        65         70
                 vv
clus              STAGE IIIB STAGE IV
  ASCL3 MUTATED            0        2
  ASCL3 WILD-TYPE         11       23
D76V3, multiclass
            clus
vv           ASCL3 MUTATED ASCL3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               2             131
  STAGE IIA              0              46
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASCL3 MUTATED     1   4   2   0
  ASCL3 WILD-TYPE 154 257  41  18
D76V4, multiclass
    clus
vv   ASCL3 MUTATED ASCL3 WILD-TYPE
  T1             1             154
  T2             4             257
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ASCL3 MUTATED     6   0     0
  ASCL3 WILD-TYPE 301  89    72
D76V5, multiclass
       clus
vv      ASCL3 MUTATED ASCL3 WILD-TYPE
  N0                6             301
  N1                0              89
  N2+N3             0              72
[1] 3 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
  ASCL3 MUTATED     3   2
  ASCL3 WILD-TYPE 324  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      3    2
  ASCL3 WILD-TYPE  324   21
   clus
vv  ASCL3 MUTATED ASCL3 WILD-TYPE
  0             3             324
  1             2              21
[1] 2 2
[1] FALSE
D76V7, binary
                 cls
clus                0   1
  ASCL3 MUTATED     2   5
  ASCL3 WILD-TYPE 257 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      2    5
  ASCL3 WILD-TYPE  257  216
        clus
vv       ASCL3 MUTATED ASCL3 WILD-TYPE
  FEMALE             2             257
  MALE               5             216
[1] 2 2
[1] FALSE
D76V8, continuous
[1] "Remove cluster labels:" "ASCL3 MUTATED"         
clus
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ASCL3 MUTATED                            0                                 4
  ASCL3 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASCL3 MUTATED                                                    3
  ASCL3 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ASCL3 MUTATED                                            0
  ASCL3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ASCL3 MUTATED                                               0
  ASCL3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ASCL3 MUTATED                                0
  ASCL3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ASCL3 MUTATED                                    0
  ASCL3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ASCL3 MUTATED                              0                             0
  ASCL3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ASCL3 MUTATED                                               0
  ASCL3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ASCL3 MUTATED                              0
  ASCL3 WILD-TYPE                            9
D76V9, multiclass
                                                    clus
vv                                                   ASCL3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ASCL3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, binary
                 cls
clus                0   1
  ASCL3 MUTATED     0   7
  ASCL3 WILD-TYPE  20 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      0    7
  ASCL3 WILD-TYPE   20  453
     clus
vv    ASCL3 MUTATED ASCL3 WILD-TYPE
  NO              0              20
  YES             7             453
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, continuous
[1] "Remove cluster labels:" "ASCL3 MUTATED"         
clus
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              1             256 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6642 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-6712      TCGA-55-6971      TCGA-55-7227      TCGA-55-7283 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7907 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-8089 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8096      TCGA-55-8097      TCGA-55-8205 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8299      TCGA-55-8301      TCGA-55-8302      TCGA-55-8506 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8511      TCGA-55-8512      TCGA-55-8514 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8615      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-62-8398 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5774      TCGA-64-5775 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-5778      TCGA-64-5779      TCGA-64-5781      TCGA-69-7761 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-7763      TCGA-69-7764      TCGA-69-7765      TCGA-69-7974 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-7979      TCGA-69-8253      TCGA-69-8255      TCGA-69-A59K 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-73-4670      TCGA-73-4675      TCGA-73-4676      TCGA-73-7498 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7031 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-80-5608      TCGA-83-5908      TCGA-86-6851      TCGA-86-7711 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-8054      TCGA-86-8055 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8281 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8673 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-91-6829      TCGA-91-6830 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7567      TCGA-95-7944      TCGA-95-7947 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8176 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A5C7      TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  ASCL3 MUTATED     4   0   1   0
  ASCL3 WILD-TYPE 306  11   3  25
D76V13, multiclass
    clus
vv   ASCL3 MUTATED ASCL3 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             1               3
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASCL3 MUTATED                                  0     0
  ASCL3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASCL3 MUTATED                           0     5
  ASCL3 WILD-TYPE                        29   372
D76V14, multiclass
                                  clus
vv                                 ASCL3 MUTATED ASCL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, binary
                 cls
clus                0   1
  ASCL3 MUTATED     0   5
  ASCL3 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      0    5
  ASCL3 WILD-TYPE    6  344
                        clus
vv                       ASCL3 MUTATED ASCL3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(77) Variable = CD84 MUTATION ANALYSIS
D77V1, survival
                sevent
clus2              0   1
  CD84 MUTATED     5   1
  CD84 WILD-TYPE 310 140
  CD84 MUTATED CD84 WILD-TYPE 
             6            450 
  CD84 MUTATED CD84 WILD-TYPE 
             1            140 
$`CD84 MUTATED`
TCGA-05-4398 TCGA-55-8089 TCGA-69-8253 TCGA-78-7145 TCGA-91-8499 TCGA-99-8032 
       47.05         3.29        14.01        27.16         1.18         1.45 

$`CD84 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30         2.93        12.56        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       23.51       163.10         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       14.27         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85        36.76         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  CD84 MUTATED CD84 WILD-TYPE 
          1.18           0.00 
  CD84 MUTATED CD84 WILD-TYPE 
         47.05         223.96 
  CD84 MUTATED CD84 WILD-TYPE 
          8.65          18.10 
[1] "1.2 - 47.0 (8.7)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D77V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CD84 MUTATED         0        3        0         1         0          0
  CD84 WILD-TYPE       4      120      133        45        67         70
                vv
clus             STAGE IIIB STAGE IV
  CD84 MUTATED            1        1
  CD84 WILD-TYPE         10       24
D77V3, multiclass
            clus
vv           CD84 MUTATED CD84 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              0            133
  STAGE IIA             1             45
  STAGE IIB             0             67
  STAGE IIIA            0             70
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD84 MUTATED     4   0   0   2
  CD84 WILD-TYPE 151 261  43  16
D77V4, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  T1            4            151
  T2            0            261
  T3            0             43
  T4            2             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"
                vv
clus              N0  N1 N2+N3
  CD84 MUTATED     3   2     1
  CD84 WILD-TYPE 304  87    71
D77V5, multiclass
       clus
vv      CD84 MUTATED CD84 WILD-TYPE
  N0               3            304
  N1               2             87
  N2+N3            1             71
[1] 3 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
  CD84 MUTATED     3   1
  CD84 WILD-TYPE 324  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      3    1
  CD84 WILD-TYPE  324   22
   clus
vv  CD84 MUTATED CD84 WILD-TYPE
  0            3            324
  1            1             22
[1] 2 2
[1] FALSE
D77V7, binary
                cls
clus               0   1
  CD84 MUTATED     4   2
  CD84 WILD-TYPE 255 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      4    2
  CD84 WILD-TYPE  255  219
        clus
vv       CD84 MUTATED CD84 WILD-TYPE
  FEMALE            4            255
  MALE              2            219
[1] 2 2
[1] FALSE
D77V8, continuous
[1] "Remove cluster labels:" "CD84 MUTATED"          
clus
  CD84 MUTATED CD84 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"CD84 WILD-TYPE" "CD84 WILD-TYPE" "CD84 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CD84 MUTATED                            0                                 2
  CD84 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CD84 MUTATED                                                    4
  CD84 WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CD84 MUTATED                                            0
  CD84 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CD84 MUTATED                                               0
  CD84 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  CD84 MUTATED                                0
  CD84 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  CD84 MUTATED                                    0
  CD84 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CD84 MUTATED                              0                             0
  CD84 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CD84 MUTATED                                               0
  CD84 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  CD84 MUTATED                              0
  CD84 WILD-TYPE                            9
D77V9, multiclass
                                                    clus
vv                                                   CD84 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   CD84 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, binary
                cls
clus               0   1
  CD84 MUTATED     0   6
  CD84 WILD-TYPE  20 454
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      0    6
  CD84 WILD-TYPE   20  454
     clus
vv    CD84 MUTATED CD84 WILD-TYPE
  NO             0             20
  YES            6            454
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, continuous
                vv
clus              R0  R1  R2  RX
  CD84 MUTATED     3   1   0   0
  CD84 WILD-TYPE 307  10   4  25
D77V13, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  R0            3            307
  R1            1             10
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD84 MUTATED                                  0     0
  CD84 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD84 MUTATED                           1     4
  CD84 WILD-TYPE                        28   373
D77V14, multiclass
                                  clus
vv                                 CD84 MUTATED CD84 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       4            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                cls
clus               0   1
  CD84 MUTATED     0   4
  CD84 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      0    4
  CD84 WILD-TYPE    6  345
                        clus
vv                       CD84 MUTATED CD84 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(78) Variable = GYPC MUTATION ANALYSIS
D78V1, survival
                sevent
clus2              0   1
  GYPC MUTATED     4   2
  GYPC WILD-TYPE 311 139
  GYPC MUTATED GYPC WILD-TYPE 
             6            450 
  GYPC MUTATED GYPC WILD-TYPE 
             2            139 
$`GYPC MUTATED`
TCGA-05-4417 TCGA-62-A46R TCGA-69-7979 TCGA-78-7147 TCGA-95-7039 TCGA-95-7947 
       14.96        56.71         2.93        19.27         1.12        15.68 

$`GYPC WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       23.51       163.10        27.16         5.69        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        6.12        23.61         1.08        19.00        17.29         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  GYPC MUTATED GYPC WILD-TYPE 
          1.12           0.00 
  GYPC MUTATED GYPC WILD-TYPE 
         56.71         223.96 
  GYPC MUTATED GYPC WILD-TYPE 
         15.32          18.10 
[1] "1.1 - 56.7 (15.3)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D78V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GYPC MUTATED         0        1        3         0         2          0
  GYPC WILD-TYPE       4      122      130        46        65         70
                vv
clus             STAGE IIIB STAGE IV
  GYPC MUTATED            0        0
  GYPC WILD-TYPE         11       25
D78V3, multiclass
            clus
vv           GYPC MUTATED GYPC WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             2             65
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GYPC MUTATED     1   4   1   0
  GYPC WILD-TYPE 154 257  42  18
D78V4, multiclass
    clus
vv   GYPC MUTATED GYPC WILD-TYPE
  T1            1            154
  T2            4            257
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  GYPC MUTATED     5   1     0
  GYPC WILD-TYPE 302  88    72
D78V5, multiclass
       clus
vv      GYPC MUTATED GYPC WILD-TYPE
  N0               5            302
  N1               1             88
  N2+N3            0             72
[1] 3 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
  GYPC MUTATED     4   0
  GYPC WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  GYPC MUTATED      4    0
  GYPC WILD-TYPE  323   23
   clus
vv  GYPC MUTATED GYPC WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D78V7, binary
                cls
clus               0   1
  GYPC MUTATED     5   1
  GYPC WILD-TYPE 254 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  GYPC MUTATED      5    1
  GYPC WILD-TYPE  254  220
        clus
vv       GYPC MUTATED GYPC WILD-TYPE
  FEMALE            5            254
  MALE              1            220
[1] 2 2
[1] FALSE
D78V8, continuous
[1] "Remove cluster labels:" "GYPC MUTATED"          
clus
  GYPC MUTATED GYPC WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46S     TCGA-62-A46U 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"GYPC WILD-TYPE" "GYPC WILD-TYPE" "GYPC WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GYPC MUTATED                            1                                 4
  GYPC WILD-TYPE                         17                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GYPC MUTATED                                                    1
  GYPC WILD-TYPE                                                293
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GYPC MUTATED                                            0
  GYPC WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GYPC MUTATED                                               0
  GYPC WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  GYPC MUTATED                                0
  GYPC WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  GYPC MUTATED                                    0
  GYPC WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GYPC MUTATED                              0                             0
  GYPC WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GYPC MUTATED                                               0
  GYPC WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  GYPC MUTATED                              0
  GYPC WILD-TYPE                            9
D78V9, multiclass
                                                    clus
vv                                                   GYPC MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   GYPC WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                cls
clus               0   1
  GYPC MUTATED     0   6
  GYPC WILD-TYPE  20 454
[1] "tbl2"
                cls
clus             [,1] [,2]
  GYPC MUTATED      0    6
  GYPC WILD-TYPE   20  454
     clus
vv    GYPC MUTATED GYPC WILD-TYPE
  NO             0             20
  YES            6            454
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, continuous
                vv
clus              R0  R1  R2  RX
  GYPC MUTATED     4   0   0   0
  GYPC WILD-TYPE 306  11   4  25
D78V13, multiclass
    clus
vv   GYPC MUTATED GYPC WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GYPC MUTATED                                  0     0
  GYPC WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GYPC MUTATED                           0     5
  GYPC WILD-TYPE                        29   372
D78V14, multiclass
                                  clus
vv                                 GYPC MUTATED GYPC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                cls
clus               0   1
  GYPC MUTATED     0   4
  GYPC WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  GYPC MUTATED      0    4
  GYPC WILD-TYPE    6  345
                        clus
vv                       GYPC MUTATED GYPC WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(79) Variable = MYH7 MUTATION ANALYSIS
D79V1, survival
                sevent
clus2              0   1
  MYH7 MUTATED    37  11
  MYH7 WILD-TYPE 278 130
  MYH7 MUTATED MYH7 WILD-TYPE 
            48            408 
  MYH7 MUTATED MYH7 WILD-TYPE 
            11            130 
$`MYH7 MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4403 TCGA-05-4427 TCGA-05-4432 TCGA-38-4625 
       19.96        45.01        19.00        26.01        25.02        97.74 
TCGA-38-7271 TCGA-44-5644 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-50-5049 
       26.30        28.37        32.45        14.60        12.03        70.55 
TCGA-50-5930 TCGA-50-5941 TCGA-53-7624 TCGA-55-1592 TCGA-55-5899 TCGA-55-6975 
        9.27        18.64        34.29        23.05         2.86         3.88 
TCGA-55-6985 TCGA-55-7815 TCGA-55-7907 TCGA-55-7995 TCGA-55-8089 TCGA-55-8092 
       40.54         1.78         0.53         0.16         3.29         5.06 
TCGA-55-8097 TCGA-55-8507 TCGA-55-8511 TCGA-55-A490 TCGA-55-A4DG TCGA-64-1676 
       15.65         0.26         0.30         1.58        19.99        56.81 
TCGA-64-5774 TCGA-64-5778 TCGA-69-7763 TCGA-78-7148 TCGA-78-7152 TCGA-78-7158 
       87.98        42.90        22.68        20.58        39.52         5.88 
TCGA-78-7539 TCGA-86-8056 TCGA-86-8073 TCGA-86-8358 TCGA-86-A4JF TCGA-91-6829 
       10.75         4.57        24.33        21.47        17.62        41.36 
TCGA-91-8499 TCGA-95-7562 TCGA-95-A4VN TCGA-97-7937 TCGA-99-8032 TCGA-MN-A4N1 
        1.18         2.86        18.18         5.95         1.45        27.19 

$`MYH7 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       24.03        47.05         8.02        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       22.03         9.04         2.04         7.40         5.98         8.68 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       44.61        14.73         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        63.72        61.28        16.44 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        30.54        13.94         9.21 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
       15.25         0.82        48.49         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        60.03        24.99       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        0.79         1.45        18.64         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       19.82        29.72        15.19        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40        20.58        19.59         0.92        15.81        20.19 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 
       13.61        39.25        40.96        29.92        20.65        55.43 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       38.37         2.04        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
       23.51       163.10        27.16         5.69        19.27        35.93 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 
       21.90        24.99        19.50        38.50        32.09        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20         8.02        53.33        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
        7.36         1.15        16.18        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         1.22        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP 
       15.68        15.65        27.29         2.76        21.40        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85        36.76         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MYH7 MUTATED MYH7 WILD-TYPE 
          0.16           0.00 
  MYH7 MUTATED MYH7 WILD-TYPE 
         97.74         223.96 
  MYH7 MUTATED MYH7 WILD-TYPE 
        18.820         17.835 
[1] "0.2 - 97.7 (18.8)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.3"
D79V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MYH7 MUTATED         0       15       17         6         6          4
  MYH7 WILD-TYPE       4      108      116        40        61         66
                vv
clus             STAGE IIIB STAGE IV
  MYH7 MUTATED            1        2
  MYH7 WILD-TYPE         10       23
D79V3, multiclass
            clus
vv           MYH7 MUTATED MYH7 WILD-TYPE
  STAGE I               0              4
  STAGE IA             15            108
  STAGE IB             17            116
  STAGE IIA             6             40
  STAGE IIB             6             61
  STAGE IIIA            4             66
  STAGE IIIB            1             10
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYH7 MUTATED    13  33   3   2
  MYH7 WILD-TYPE 142 228  40  16
D79V4, multiclass
    clus
vv   MYH7 MUTATED MYH7 WILD-TYPE
  T1           13            142
  T2           33            228
  T3            3             40
  T4            2             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"
                vv
clus              N0  N1 N2+N3
  MYH7 MUTATED    36   9     5
  MYH7 WILD-TYPE 271  80    67
D79V5, multiclass
       clus
vv      MYH7 MUTATED MYH7 WILD-TYPE
  N0              36            271
  N1               9             80
  N2+N3            5             67
[1] 3 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
  MYH7 MUTATED    34   2
  MYH7 WILD-TYPE 293  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH7 MUTATED     34    2
  MYH7 WILD-TYPE  293   21
   clus
vv  MYH7 MUTATED MYH7 WILD-TYPE
  0           34            293
  1            2             21
[1] 2 2
[1] FALSE
D79V7, binary
                cls
clus               0   1
  MYH7 MUTATED    19  32
  MYH7 WILD-TYPE 240 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH7 MUTATED     19   32
  MYH7 WILD-TYPE  240  189
        clus
vv       MYH7 MUTATED MYH7 WILD-TYPE
  FEMALE           19            240
  MALE             32            189
[1] 2 2
[1] FALSE
D79V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MYH7 MUTATED                            0                                13
  MYH7 WILD-TYPE                         18                                89
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MYH7 MUTATED                                                   32
  MYH7 WILD-TYPE                                                262
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MYH7 MUTATED                                            0
  MYH7 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MYH7 MUTATED                                               3
  MYH7 WILD-TYPE                                            16
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MYH7 MUTATED                                0
  MYH7 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MYH7 MUTATED                                    1
  MYH7 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MYH7 MUTATED                              0                             1
  MYH7 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MYH7 MUTATED                                               1
  MYH7 WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MYH7 MUTATED                              0
  MYH7 WILD-TYPE                            9
D79V9, multiclass
                                                    clus
vv                                                   MYH7 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            13
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           32
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MYH7 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            262
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, binary
                cls
clus               0   1
  MYH7 MUTATED     3  48
  MYH7 WILD-TYPE  17 412
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH7 MUTATED      3   48
  MYH7 WILD-TYPE   17  412
     clus
vv    MYH7 MUTATED MYH7 WILD-TYPE
  NO             3             17
  YES           48            412
[1] 2 2
[1] FALSE
D79V11, continuous
D79V12, continuous
                vv
clus              R0  R1  R2  RX
  MYH7 MUTATED    36   1   1   2
  MYH7 WILD-TYPE 274  10   3  23
D79V13, multiclass
    clus
vv   MYH7 MUTATED MYH7 WILD-TYPE
  R0           36            274
  R1            1             10
  R2            1              3
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH7 MUTATED                                  0     0
  MYH7 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH7 MUTATED                           2    40
  MYH7 WILD-TYPE                        27   337
D79V14, multiclass
                                  clus
vv                                 MYH7 MUTATED MYH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                      40            337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                cls
clus               0   1
  MYH7 MUTATED     1  34
  MYH7 WILD-TYPE   5 315
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH7 MUTATED      1   34
  MYH7 WILD-TYPE    5  315
                        clus
vv                       MYH7 MUTATED MYH7 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           34            315
[1] 2 2
[1] FALSE

Clustering(80) Variable = UROC1 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  UROC1 MUTATED    14   1
  UROC1 WILD-TYPE 301 140
  UROC1 MUTATED UROC1 WILD-TYPE 
             15             441 
  UROC1 MUTATED UROC1 WILD-TYPE 
              1             140 
$`UROC1 MUTATED`
TCGA-05-4405 TCGA-05-4430 TCGA-44-5643 TCGA-44-6147 TCGA-49-6767 TCGA-50-5049 
       20.05        25.02        33.30        27.78        22.26        70.55 
TCGA-53-7813 TCGA-55-6968 TCGA-55-8506 TCGA-55-A490 TCGA-64-1676 TCGA-69-7978 
       13.94        42.51         0.36         1.58        56.81         2.30 
TCGA-86-A456 TCGA-J2-8194 TCGA-MN-A4N4 
       13.32        23.80        38.63 

$`UROC1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       37.15        38.24        34.06         6.25        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
       12.59        23.77        10.78         9.93        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       14.63        12.13        29.26        17.16        11.64        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       30.54         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65         0.79        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
       72.30        13.61        39.25        40.96        29.92        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45         5.59        24.30        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  UROC1 MUTATED UROC1 WILD-TYPE 
           0.36            0.00 
  UROC1 MUTATED UROC1 WILD-TYPE 
          70.55          223.96 
  UROC1 MUTATED UROC1 WILD-TYPE 
          23.80           17.75 
[1] "0.4 - 70.5 (23.8)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "5.6"
D80V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  UROC1 MUTATED         0        5        2         1         4          1
  UROC1 WILD-TYPE       4      118      131        45        63         69
                 vv
clus              STAGE IIIB STAGE IV
  UROC1 MUTATED            1        1
  UROC1 WILD-TYPE         10       24
D80V3, multiclass
            clus
vv           UROC1 MUTATED UROC1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               2             131
  STAGE IIA              1              45
  STAGE IIB              4              63
  STAGE IIIA             1              69
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UROC1 MUTATED     5   6   3   1
  UROC1 WILD-TYPE 150 255  40  17
D80V4, multiclass
    clus
vv   UROC1 MUTATED UROC1 WILD-TYPE
  T1             5             150
  T2             6             255
  T3             3              40
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  UROC1 MUTATED    12   1     1
  UROC1 WILD-TYPE 295  88    71
D80V5, multiclass
       clus
vv      UROC1 MUTATED UROC1 WILD-TYPE
  N0               12             295
  N1                1              88
  N2+N3             1              71
[1] 3 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
  UROC1 MUTATED     9   1
  UROC1 WILD-TYPE 318  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UROC1 MUTATED      9    1
  UROC1 WILD-TYPE  318   22
   clus
vv  UROC1 MUTATED UROC1 WILD-TYPE
  0             9             318
  1             1              22
[1] 2 2
[1] FALSE
D80V7, binary
                 cls
clus                0   1
  UROC1 MUTATED     8   7
  UROC1 WILD-TYPE 251 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UROC1 MUTATED      8    7
  UROC1 WILD-TYPE  251  214
        clus
vv       UROC1 MUTATED UROC1 WILD-TYPE
  FEMALE             8             251
  MALE               7             214
[1] 2 2
[1] FALSE
D80V8, continuous
[1] "Remove cluster labels:" "UROC1 MUTATED"         
clus
  UROC1 MUTATED UROC1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N5 
"UROC1 WILD-TYPE" "UROC1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  UROC1 MUTATED                            0                                 4
  UROC1 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  UROC1 MUTATED                                                    9
  UROC1 WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  UROC1 MUTATED                                            0
  UROC1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  UROC1 MUTATED                                               1
  UROC1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  UROC1 MUTATED                                0
  UROC1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  UROC1 MUTATED                                    0
  UROC1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  UROC1 MUTATED                              0                             1
  UROC1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  UROC1 MUTATED                                               0
  UROC1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  UROC1 MUTATED                              0
  UROC1 WILD-TYPE                            9
D80V9, multiclass
                                                    clus
vv                                                   UROC1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   UROC1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, binary
                 cls
clus                0   1
  UROC1 MUTATED     2  13
  UROC1 WILD-TYPE  18 447
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UROC1 MUTATED      2   13
  UROC1 WILD-TYPE   18  447
     clus
vv    UROC1 MUTATED UROC1 WILD-TYPE
  NO              2              18
  YES            13             447
[1] 2 2
[1] FALSE
D80V11, continuous
D80V12, continuous
                 vv
clus               R0  R1  R2  RX
  UROC1 MUTATED     8   0   0   0
  UROC1 WILD-TYPE 302  11   4  25
D80V13, multiclass
    clus
vv   UROC1 MUTATED UROC1 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UROC1 MUTATED                                  0     1
  UROC1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UROC1 MUTATED                           1    11
  UROC1 WILD-TYPE                        28   366
D80V14, multiclass
                                  clus
vv                                 UROC1 MUTATED UROC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                 cls
clus                0   1
  UROC1 MUTATED     0  12
  UROC1 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UROC1 MUTATED      0   12
  UROC1 WILD-TYPE    6  337
                        clus
vv                       UROC1 MUTATED UROC1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(81) Variable = HSF5 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  HSF5 MUTATED    10   1
  HSF5 WILD-TYPE 305 140
  HSF5 MUTATED HSF5 WILD-TYPE 
            11            445 
  HSF5 MUTATED HSF5 WILD-TYPE 
             1            140 
$`HSF5 MUTATED`
TCGA-05-4382 TCGA-05-4427 TCGA-55-8621 TCGA-62-A471 TCGA-69-7978 TCGA-69-8253 
       19.96        26.01        16.93        40.96         2.30        14.01 
TCGA-86-7711 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-J2-A4AG 
       34.39         1.12         1.22        18.67        16.44 

$`HSF5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61         2.17        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 
       67.96        72.30        13.61        39.25        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.93        12.56 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 
      110.50        27.09        12.36         5.88        31.13        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       19.00        17.29         2.86        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       23.80        18.08        35.47        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  HSF5 MUTATED HSF5 WILD-TYPE 
          1.12           0.00 
  HSF5 MUTATED HSF5 WILD-TYPE 
         40.96         223.96 
  HSF5 MUTATED HSF5 WILD-TYPE 
         16.93          18.08 
[1] "1.1 - 41.0 (16.9)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.4"
D81V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HSF5 MUTATED         0        3        2         2         5          1
  HSF5 WILD-TYPE       4      120      131        44        62         69
                vv
clus             STAGE IIIB STAGE IV
  HSF5 MUTATED            0        0
  HSF5 WILD-TYPE         11       25
D81V3, multiclass
            clus
vv           HSF5 MUTATED HSF5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              2            131
  STAGE IIA             2             44
  STAGE IIB             5             62
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HSF5 MUTATED     4   8   1   0
  HSF5 WILD-TYPE 151 253  42  18
D81V4, multiclass
    clus
vv   HSF5 MUTATED HSF5 WILD-TYPE
  T1            4            151
  T2            8            253
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  HSF5 MUTATED     6   6     1
  HSF5 WILD-TYPE 301  83    71
D81V5, multiclass
       clus
vv      HSF5 MUTATED HSF5 WILD-TYPE
  N0               6            301
  N1               6             83
  N2+N3            1             71
[1] 3 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
  HSF5 MUTATED     7   0
  HSF5 WILD-TYPE 320  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      7    0
  HSF5 WILD-TYPE  320   23
   clus
vv  HSF5 MUTATED HSF5 WILD-TYPE
  0            7            320
  1            0             23
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus               0   1
  HSF5 MUTATED     7   6
  HSF5 WILD-TYPE 252 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      7    6
  HSF5 WILD-TYPE  252  215
        clus
vv       HSF5 MUTATED HSF5 WILD-TYPE
  FEMALE            7            252
  MALE              6            215
[1] 2 2
[1] FALSE
D81V8, continuous
[1] "Remove cluster labels:" "HSF5 MUTATED"          
clus
  HSF5 MUTATED HSF5 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7713     TCGA-86-7714 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8055     TCGA-86-8056 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"HSF5 WILD-TYPE" "HSF5 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HSF5 MUTATED                            0                                 8
  HSF5 WILD-TYPE                         18                                94
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HSF5 MUTATED                                                    5
  HSF5 WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HSF5 MUTATED                                            0
  HSF5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HSF5 MUTATED                                               0
  HSF5 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  HSF5 MUTATED                                0
  HSF5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  HSF5 MUTATED                                    0
  HSF5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HSF5 MUTATED                              0                             0
  HSF5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HSF5 MUTATED                                               0
  HSF5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  HSF5 MUTATED                              0
  HSF5 WILD-TYPE                            9
D81V9, multiclass
                                                    clus
vv                                                   HSF5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   HSF5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, binary
                cls
clus               0   1
  HSF5 MUTATED     0  13
  HSF5 WILD-TYPE  20 447
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      0   13
  HSF5 WILD-TYPE   20  447
     clus
vv    HSF5 MUTATED HSF5 WILD-TYPE
  NO             0             20
  YES           13            447
[1] 2 2
[1] FALSE
D81V11, continuous
D81V12, continuous
                vv
clus              R0  R1  R2  RX
  HSF5 MUTATED     7   0   0   1
  HSF5 WILD-TYPE 303  11   4  24
D81V13, multiclass
    clus
vv   HSF5 MUTATED HSF5 WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSF5 MUTATED                                  0     0
  HSF5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HSF5 MUTATED                           1     8
  HSF5 WILD-TYPE                        28   369
D81V14, multiclass
                                  clus
vv                                 HSF5 MUTATED HSF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V15, binary
                cls
clus               0   1
  HSF5 MUTATED     1   8
  HSF5 WILD-TYPE   5 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      1    8
  HSF5 WILD-TYPE    5  341
                        clus
vv                       HSF5 MUTATED HSF5 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(82) Variable = HSPA8 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  HSPA8 MUTATED     5   4
  HSPA8 WILD-TYPE 310 137
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             447 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              4             137 
$`HSPA8 MUTATED`
TCGA-50-5946 TCGA-53-7624 TCGA-55-1592 TCGA-69-7978 TCGA-73-4666 TCGA-78-7147 
       22.55        34.29        23.05         2.30        26.30        19.27 
TCGA-78-7542 TCGA-86-8056 TCGA-86-8358 
       10.55         4.57        21.47 

$`HSPA8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 
       15.12        18.64        29.03        25.12        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        23.38        29.98        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  HSPA8 MUTATED HSPA8 WILD-TYPE 
            2.3             0.0 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
          34.29          223.96 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
          21.47           17.92 
[1] "2.3 - 34.3 (21.5)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "2.1"
D82V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HSPA8 MUTATED         0        2        2         0         2          1
  HSPA8 WILD-TYPE       4      121      131        46        65         69
                 vv
clus              STAGE IIIB STAGE IV
  HSPA8 MUTATED            0        2
  HSPA8 WILD-TYPE         11       23
D82V3, multiclass
            clus
vv           HSPA8 MUTATED HSPA8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               2             131
  STAGE IIA              0              46
  STAGE IIB              2              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HSPA8 MUTATED     2   6   0   1
  HSPA8 WILD-TYPE 153 255  43  17
D82V4, multiclass
    clus
vv   HSPA8 MUTATED HSPA8 WILD-TYPE
  T1             2             153
  T2             6             255
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  HSPA8 MUTATED     7   2     0
  HSPA8 WILD-TYPE 300  87    72
D82V5, multiclass
       clus
vv      HSPA8 MUTATED HSPA8 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             0              72
[1] 3 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
  HSPA8 MUTATED     5   2
  HSPA8 WILD-TYPE 322  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      5    2
  HSPA8 WILD-TYPE  322   21
   clus
vv  HSPA8 MUTATED HSPA8 WILD-TYPE
  0             5             322
  1             2              21
[1] 2 2
[1] FALSE
D82V7, binary
                 cls
clus                0   1
  HSPA8 MUTATED     4   5
  HSPA8 WILD-TYPE 255 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      4    5
  HSPA8 WILD-TYPE  255  216
        clus
vv       HSPA8 MUTATED HSPA8 WILD-TYPE
  FEMALE             4             255
  MALE               5             216
[1] 2 2
[1] FALSE
D82V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HSPA8 MUTATED                            0                                 3
  HSPA8 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HSPA8 MUTATED                                                    6
  HSPA8 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HSPA8 MUTATED                                            0
  HSPA8 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HSPA8 MUTATED                                               0
  HSPA8 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HSPA8 MUTATED                                0
  HSPA8 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HSPA8 MUTATED                                    0
  HSPA8 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HSPA8 MUTATED                              0                             0
  HSPA8 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HSPA8 MUTATED                                               0
  HSPA8 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HSPA8 MUTATED                              0
  HSPA8 WILD-TYPE                            9
D82V9, multiclass
                                                    clus
vv                                                   HSPA8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HSPA8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, binary
                 cls
clus                0   1
  HSPA8 MUTATED     1   8
  HSPA8 WILD-TYPE  19 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      1    8
  HSPA8 WILD-TYPE   19  452
     clus
vv    HSPA8 MUTATED HSPA8 WILD-TYPE
  NO              1              19
  YES             8             452
[1] 2 2
[1] FALSE
D82V11, continuous
D82V12, continuous
                 vv
clus               R0  R1  R2  RX
  HSPA8 MUTATED     7   0   0   0
  HSPA8 WILD-TYPE 303  11   4  25
D82V13, multiclass
    clus
vv   HSPA8 MUTATED HSPA8 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSPA8 MUTATED                                  0     0
  HSPA8 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HSPA8 MUTATED                           0     9
  HSPA8 WILD-TYPE                        29   368
D82V14, multiclass
                                  clus
vv                                 HSPA8 MUTATED HSPA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, binary
                 cls
clus                0   1
  HSPA8 MUTATED     1   5
  HSPA8 WILD-TYPE   5 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      1    5
  HSPA8 WILD-TYPE    5  344
                        clus
vv                       HSPA8 MUTATED HSPA8 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(83) Variable = HTRA1 MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2               0   1
  HTRA1 MUTATED     6   3
  HTRA1 WILD-TYPE 309 138
  HTRA1 MUTATED HTRA1 WILD-TYPE 
              9             447 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
              3             138 
$`HTRA1 MUTATED`
TCGA-05-5425 TCGA-49-6745 TCGA-55-8507 TCGA-78-7156 TCGA-86-8055 TCGA-99-8025 
       29.00        17.16         0.26        32.09         4.08        34.85 
TCGA-MN-A4N4 TCGA-NJ-A4YQ TCGA-O1-A52J 
       38.63        29.13        59.11 

$`HTRA1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.36         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       16.70        24.49         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.26         0.43        19.82 

  HTRA1 MUTATED HTRA1 WILD-TYPE 
           0.26            0.00 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
          59.11          223.96 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
          29.13           17.92 
[1] "0.3 - 59.1 (29.1)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.1"
D83V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HTRA1 MUTATED         0        4        1         1         1          2
  HTRA1 WILD-TYPE       4      119      132        45        66         68
                 vv
clus              STAGE IIIB STAGE IV
  HTRA1 MUTATED            0        1
  HTRA1 WILD-TYPE         11       24
D83V3, multiclass
            clus
vv           HTRA1 MUTATED HTRA1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               1             132
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HTRA1 MUTATED     4   4   1   1
  HTRA1 WILD-TYPE 151 257  42  17
D83V4, multiclass
    clus
vv   HTRA1 MUTATED HTRA1 WILD-TYPE
  T1             4             151
  T2             4             257
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  HTRA1 MUTATED     5   3     2
  HTRA1 WILD-TYPE 302  86    70
D83V5, multiclass
       clus
vv      HTRA1 MUTATED HTRA1 WILD-TYPE
  N0                5             302
  N1                3              86
  N2+N3             2              70
[1] 3 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
  HTRA1 MUTATED     7   1
  HTRA1 WILD-TYPE 320  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      7    1
  HTRA1 WILD-TYPE  320   22
   clus
vv  HTRA1 MUTATED HTRA1 WILD-TYPE
  0             7             320
  1             1              22
[1] 2 2
[1] FALSE
D83V7, binary
                 cls
clus                0   1
  HTRA1 MUTATED     3   7
  HTRA1 WILD-TYPE 256 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      3    7
  HTRA1 WILD-TYPE  256  214
        clus
vv       HTRA1 MUTATED HTRA1 WILD-TYPE
  FEMALE             3             256
  MALE               7             214
[1] 2 2
[1] FALSE
D83V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HTRA1 MUTATED                            0                                 2
  HTRA1 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HTRA1 MUTATED                                                    8
  HTRA1 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HTRA1 MUTATED                                            0
  HTRA1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HTRA1 MUTATED                                               0
  HTRA1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HTRA1 MUTATED                                0
  HTRA1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HTRA1 MUTATED                                    0
  HTRA1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HTRA1 MUTATED                              0                             0
  HTRA1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HTRA1 MUTATED                                               0
  HTRA1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HTRA1 MUTATED                              0
  HTRA1 WILD-TYPE                            9
D83V9, multiclass
                                                    clus
vv                                                   HTRA1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HTRA1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V10, binary
                 cls
clus                0   1
  HTRA1 MUTATED     0  10
  HTRA1 WILD-TYPE  20 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      0   10
  HTRA1 WILD-TYPE   20  450
     clus
vv    HTRA1 MUTATED HTRA1 WILD-TYPE
  NO              0              20
  YES            10             450
[1] 2 2
[1] FALSE
D83V11, continuous
D83V12, continuous
                 vv
clus               R0  R1  R2  RX
  HTRA1 MUTATED     7   0   0   1
  HTRA1 WILD-TYPE 303  11   4  24
D83V13, multiclass
    clus
vv   HTRA1 MUTATED HTRA1 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HTRA1 MUTATED                                  0     0
  HTRA1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HTRA1 MUTATED                           1     7
  HTRA1 WILD-TYPE                        28   370
D83V14, multiclass
                                  clus
vv                                 HTRA1 MUTATED HTRA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V15, binary
                 cls
clus                0   1
  HTRA1 MUTATED     0   6
  HTRA1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      0    6
  HTRA1 WILD-TYPE    6  343
                        clus
vv                       HTRA1 MUTATED HTRA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(84) Variable = DST MUTATION ANALYSIS
D84V1, survival
               sevent
clus2             0   1
  DST MUTATED    66  20
  DST WILD-TYPE 249 121
  DST MUTATED DST WILD-TYPE 
           86           370 
  DST MUTATED DST WILD-TYPE 
           20           121 
$`DST MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4420 TCGA-05-4424 
       19.96        14.01         9.96        47.05        29.98        30.02 
TCGA-05-4427 TCGA-05-4430 TCGA-05-5425 TCGA-38-4626 TCGA-44-3396 TCGA-44-3398 
       26.01        25.02        29.00       120.79        37.15        38.24 
TCGA-44-3918 TCGA-44-5644 TCGA-44-6778 TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 
       34.06        28.37        61.28        12.03        18.87        29.00 
TCGA-44-8119 TCGA-49-4487 TCGA-49-4507 TCGA-49-6743 TCGA-49-6767 TCGA-50-5045 
        3.25        28.11         8.81        12.13        22.26        71.47 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5946 TCGA-50-7109 TCGA-55-6983 TCGA-55-6985 
       14.27        78.67        22.55        10.13        60.03        40.54 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 TCGA-55-7907 TCGA-55-7994 TCGA-55-7995 
        0.59         1.15         1.32         0.53        19.82         0.16 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 
        0.13        23.64        17.98         1.08         2.17        15.42 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8511 TCGA-55-8512 TCGA-62-8395 
        0.76         0.36         0.26         0.30         0.10        39.98 
TCGA-62-A46O TCGA-64-5779 TCGA-67-3771 TCGA-67-6215 TCGA-69-7974 TCGA-69-7980 
       47.80        28.41        20.05         5.72         6.05        12.56 
TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 TCGA-73-4668 TCGA-73-7498 TCGA-78-7148 
       14.01         7.04        23.38        15.35        39.09        20.58 
TCGA-78-7155 TCGA-78-7220 TCGA-78-8662 TCGA-86-6851 TCGA-86-7714 TCGA-86-8073 
       38.50        26.53       110.50         5.88        20.55        24.33 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8673 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
       15.85        21.47        14.96        41.36        10.19         2.60 
TCGA-95-7567 TCGA-95-7947 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-A4M0 
       18.67        15.68        43.79        25.48         0.59        21.44 
TCGA-99-7458 TCGA-99-8025 TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MP-A4TD TCGA-NJ-A4YF 
       24.56        34.85        19.00        38.63        10.09        71.05 
TCGA-NJ-A4YQ TCGA-NJ-A55R 
       29.13        19.82 

$`DST WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
        8.02        19.00        20.05         2.99        14.96         9.01 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       12.00        21.99        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
       15.02         4.96        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        5.98         8.68        97.74        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3919 TCGA-44-4112 
       46.98        13.15        24.36        42.77         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
       23.15        21.63        23.18        63.72        32.45        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 
       14.60        19.46         7.17        36.07        17.59        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       35.54        46.72        14.07        32.84        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       55.89        14.63        29.26        17.16        11.64        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        40.60        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21        41.69         0.72        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 
        7.79         2.20        45.34        32.71        24.99       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
       70.26         1.74         7.99         0.20         0.13         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 
        1.45        18.64         6.48        17.65         6.15        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 
       15.19         3.29        19.66        19.73         5.06        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 TCGA-55-8510 
        1.51        22.16         1.45         0.95         0.49        17.72 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
        4.57        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
       87.98         2.04        42.90        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.04         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 
       13.61         5.42         7.56         2.30         2.93        13.45 
TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 
        4.24         2.01         0.10        52.60        29.98        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 
        4.31         1.32         5.39         1.25        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        19.27        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
        7.07       104.19       223.96         8.48        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      214.62        39.75        77.59        10.55        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        13.87        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.65        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
       27.58         0.62        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       26.47        10.62         1.97        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 
       19.89        31.69        64.60        63.52         5.95         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.58        20.19        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        20.68        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81         0.20        27.19         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59        31.23         2.43        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        1.64         0.26         0.43        59.11 

  DST MUTATED DST WILD-TYPE 
          0.1           0.0 
  DST MUTATED DST WILD-TYPE 
       120.79        223.96 
  DST MUTATED DST WILD-TYPE 
       20.005        17.605 
[1] "0.1 - 120.8 (20.0)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.5"
D84V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DST MUTATED         2       21       24         7        14         15
  DST WILD-TYPE       2      102      109        39        53         55
               vv
clus            STAGE IIIB STAGE IV
  DST MUTATED            3        3
  DST WILD-TYPE          8       22
D84V3, multiclass
            clus
vv           DST MUTATED DST WILD-TYPE
  STAGE I              2             2
  STAGE IA            21           102
  STAGE IB            24           109
  STAGE IIA            7            39
  STAGE IIB           14            53
  STAGE IIIA          15            55
  STAGE IIIB           3             8
  STAGE IV             3            22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DST MUTATED    30  44  11   4
  DST WILD-TYPE 125 217  32  14
D84V4, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  T1          30           125
  T2          44           217
  T3          11            32
  T4           4            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"
               vv
clus             N0  N1 N2+N3
  DST MUTATED    57  16    16
  DST WILD-TYPE 250  73    56
D84V5, multiclass
       clus
vv      DST MUTATED DST WILD-TYPE
  N0             57           250
  N1             16            73
  N2+N3          16            56
[1] 3 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
  DST MUTATED    61   3
  DST WILD-TYPE 266  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     61    3
  DST WILD-TYPE  266   20
   clus
vv  DST MUTATED DST WILD-TYPE
  0          61           266
  1           3            20
[1] 2 2
[1] FALSE
D84V7, binary
               cls
clus              0   1
  DST MUTATED    51  38
  DST WILD-TYPE 208 183
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     51   38
  DST WILD-TYPE  208  183
        clus
vv       DST MUTATED DST WILD-TYPE
  FEMALE          51           208
  MALE            38           183
[1] 2 2
[1] FALSE
D84V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DST MUTATED                            2                                22
  DST WILD-TYPE                         16                                80
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DST MUTATED                                                   51
  DST WILD-TYPE                                                243
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DST MUTATED                                            0
  DST WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DST MUTATED                                               9
  DST WILD-TYPE                                            10
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  DST MUTATED                                1
  DST WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  DST MUTATED                                    1                            0
  DST WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  DST MUTATED                               2
  DST WILD-TYPE                            20
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DST MUTATED                                               0
  DST WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  DST MUTATED                              1
  DST WILD-TYPE                            8
D84V9, multiclass
                                                    clus
vv                                                   DST MUTATED DST WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   2            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           22            80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          51           243
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                9            10
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           1             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                2            20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 1             8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V10, binary
               cls
clus              0   1
  DST MUTATED     6  83
  DST WILD-TYPE  14 377
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED      6   83
  DST WILD-TYPE   14  377
     clus
vv    DST MUTATED DST WILD-TYPE
  NO            6            14
  YES          83           377
[1] 2 2
[1] FALSE
D84V11, continuous
D84V12, continuous
               vv
clus             R0  R1  R2  RX
  DST MUTATED    59   1   1   4
  DST WILD-TYPE 251  10   3  21
D84V13, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  R0          59           251
  R1           1            10
  R2           1             3
  RX           4            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DST MUTATED                                  1     0
  DST WILD-TYPE                                0     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DST MUTATED                          10    65
  DST WILD-TYPE                        19   312
D84V14, multiclass
                                  clus
vv                                 DST MUTATED DST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                 10            19
  WHITE                                     65           312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V15, binary
               cls
clus              0   1
  DST MUTATED     1  64
  DST WILD-TYPE   5 285
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED      1   64
  DST WILD-TYPE    5  285
                        clus
vv                       DST MUTATED DST WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          64           285
[1] 2 2
[1] FALSE

Clustering(85) Variable = SRMS MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  SRMS MUTATED     7   3
  SRMS WILD-TYPE 308 138
  SRMS MUTATED SRMS WILD-TYPE 
            10            446 
  SRMS MUTATED SRMS WILD-TYPE 
             3            138 
$`SRMS MUTATED`
TCGA-55-8507 TCGA-73-4668 TCGA-78-7155 TCGA-78-7539 TCGA-86-A4JF TCGA-91-6829 
        0.26        15.35        38.50        10.75        17.62        41.36 
TCGA-97-8179 TCGA-MN-A4N5 TCGA-MP-A4T4 TCGA-NJ-A4YF 
       14.30         2.76        86.04        71.05 

$`SRMS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       29.98        26.30         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       17.92         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
       38.63        86.14        58.45        49.35        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SRMS MUTATED SRMS WILD-TYPE 
          0.26           0.00 
  SRMS MUTATED SRMS WILD-TYPE 
         86.04         223.96 
  SRMS MUTATED SRMS WILD-TYPE 
        16.485         18.100 
[1] "0.3 - 86.0 (16.5)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D85V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SRMS MUTATED         0        4        2         1         3          0
  SRMS WILD-TYPE       4      119      131        45        64         70
                vv
clus             STAGE IIIB STAGE IV
  SRMS MUTATED            0        0
  SRMS WILD-TYPE         11       25
D85V3, multiclass
            clus
vv           SRMS MUTATED SRMS WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              2            131
  STAGE IIA             1             45
  STAGE IIB             3             64
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SRMS MUTATED     4   5   1   0
  SRMS WILD-TYPE 151 256  42  18
D85V4, multiclass
    clus
vv   SRMS MUTATED SRMS WILD-TYPE
  T1            4            151
  T2            5            256
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  SRMS MUTATED     8   2     0
  SRMS WILD-TYPE 299  87    72
D85V5, multiclass
       clus
vv      SRMS MUTATED SRMS WILD-TYPE
  N0               8            299
  N1               2             87
  N2+N3            0             72
[1] 3 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
  SRMS MUTATED     8   0
  SRMS WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRMS MUTATED      8    0
  SRMS WILD-TYPE  319   23
   clus
vv  SRMS MUTATED SRMS WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D85V7, binary
                cls
clus               0   1
  SRMS MUTATED     4   6
  SRMS WILD-TYPE 255 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRMS MUTATED      4    6
  SRMS WILD-TYPE  255  215
        clus
vv       SRMS MUTATED SRMS WILD-TYPE
  FEMALE            4            255
  MALE              6            215
[1] 2 2
[1] FALSE
D85V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SRMS MUTATED                            1                                 2
  SRMS WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SRMS MUTATED                                                    5
  SRMS WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SRMS MUTATED                                            0
  SRMS WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SRMS MUTATED                                               1
  SRMS WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SRMS MUTATED                                0
  SRMS WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SRMS MUTATED                                    1
  SRMS WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SRMS MUTATED                              0                             0
  SRMS WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SRMS MUTATED                                               0
  SRMS WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SRMS MUTATED                              0
  SRMS WILD-TYPE                            9
D85V9, multiclass
                                                    clus
vv                                                   SRMS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SRMS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V10, binary
                cls
clus               0   1
  SRMS MUTATED     0  10
  SRMS WILD-TYPE  20 450
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRMS MUTATED      0   10
  SRMS WILD-TYPE   20  450
     clus
vv    SRMS MUTATED SRMS WILD-TYPE
  NO             0             20
  YES           10            450
[1] 2 2
[1] FALSE
D85V11, continuous
D85V12, continuous
                vv
clus              R0  R1  R2  RX
  SRMS MUTATED     8   0   0   0
  SRMS WILD-TYPE 302  11   4  25
D85V13, multiclass
    clus
vv   SRMS MUTATED SRMS WILD-TYPE
  R0            8            302
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRMS MUTATED                                  1     0
  SRMS WILD-TYPE                                0     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SRMS MUTATED                           1     8
  SRMS WILD-TYPE                        28   369
D85V14, multiclass
                                  clus
vv                                 SRMS MUTATED SRMS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V15, binary
                cls
clus               0   1
  SRMS MUTATED     0   7
  SRMS WILD-TYPE   6 342
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRMS MUTATED      0    7
  SRMS WILD-TYPE    6  342
                        clus
vv                       SRMS MUTATED SRMS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            7            342
[1] 2 2
[1] FALSE

Clustering(86) Variable = PTPRU MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2               0   1
  PTPRU MUTATED    13   5
  PTPRU WILD-TYPE 302 136
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             438 
  PTPRU MUTATED PTPRU WILD-TYPE 
              5             136 
$`PTPRU MUTATED`
TCGA-05-4397 TCGA-05-4420 TCGA-44-8117 TCGA-49-6744 TCGA-55-6982 TCGA-55-7995 
       24.03        29.98        12.66        29.26        32.71         0.16 
TCGA-55-8506 TCGA-62-A46O TCGA-67-3771 TCGA-69-7978 TCGA-73-4668 TCGA-78-7539 
        0.36        47.80        20.05         2.30        15.35        10.75 
TCGA-86-8279 TCGA-91-6829 TCGA-91-6836 TCGA-91-8499 TCGA-J2-A4AD TCGA-MN-A4N4 
       15.85        41.36        13.71         1.18        18.08        38.63 

$`PTPRU WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        17.59        23.64         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       55.89        14.63        12.13        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
        0.53         6.48        17.65         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        0.10        52.60        23.38        29.98        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.65        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       17.62        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
        2.60        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       23.80        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  PTPRU MUTATED PTPRU WILD-TYPE 
           0.16            0.00 
  PTPRU MUTATED PTPRU WILD-TYPE 
          47.80          223.96 
  PTPRU MUTATED PTPRU WILD-TYPE 
         16.965          18.050 
[1] "0.2 - 47.8 (17.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D86V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PTPRU MUTATED         0        5        5         3         5          0
  PTPRU WILD-TYPE       4      118      128        43        62         70
                 vv
clus              STAGE IIIB STAGE IV
  PTPRU MUTATED            0        0
  PTPRU WILD-TYPE         11       25
D86V3, multiclass
            clus
vv           PTPRU MUTATED PTPRU WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               5             128
  STAGE IIA              3              43
  STAGE IIB              5              62
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRU MUTATED     5  12   1   0
  PTPRU WILD-TYPE 150 249  42  18
D86V4, multiclass
    clus
vv   PTPRU MUTATED PTPRU WILD-TYPE
  T1             5             150
  T2            12             249
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PTPRU MUTATED    12   6     0
  PTPRU WILD-TYPE 295  83    72
D86V5, multiclass
       clus
vv      PTPRU MUTATED PTPRU WILD-TYPE
  N0               12             295
  N1                6              83
  N2+N3             0              72
[1] 3 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
  PTPRU MUTATED    11   0
  PTPRU WILD-TYPE 316  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     11    0
  PTPRU WILD-TYPE  316   23
   clus
vv  PTPRU MUTATED PTPRU WILD-TYPE
  0            11             316
  1             0              23
[1] 2 2
[1] FALSE
D86V7, binary
                 cls
clus                0   1
  PTPRU MUTATED    12   6
  PTPRU WILD-TYPE 247 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     12    6
  PTPRU WILD-TYPE  247  215
        clus
vv       PTPRU MUTATED PTPRU WILD-TYPE
  FEMALE            12             247
  MALE               6             215
[1] 2 2
[1] FALSE
D86V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PTPRU MUTATED                            0                                 5
  PTPRU WILD-TYPE                         18                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTPRU MUTATED                                                   11
  PTPRU WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PTPRU MUTATED                                            0
  PTPRU WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PTPRU MUTATED                                               1
  PTPRU WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PTPRU MUTATED                                0
  PTPRU WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PTPRU MUTATED                                    1
  PTPRU WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PTPRU MUTATED                              0                             0
  PTPRU WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PTPRU MUTATED                                               0
  PTPRU WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PTPRU MUTATED                              0
  PTPRU WILD-TYPE                            9
D86V9, multiclass
                                                    clus
vv                                                   PTPRU MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PTPRU WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V10, binary
                 cls
clus                0   1
  PTPRU MUTATED     0  18
  PTPRU WILD-TYPE  20 442
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED      0   18
  PTPRU WILD-TYPE   20  442
     clus
vv    PTPRU MUTATED PTPRU WILD-TYPE
  NO              0              20
  YES            18             442
[1] 2 2
[1] FALSE
D86V11, continuous
D86V12, continuous
                 vv
clus               R0  R1  R2  RX
  PTPRU MUTATED    12   0   0   1
  PTPRU WILD-TYPE 298  11   4  24
D86V13, multiclass
    clus
vv   PTPRU MUTATED PTPRU WILD-TYPE
  R0            12             298
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRU MUTATED                                  1     0
  PTPRU WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRU MUTATED                           1    14
  PTPRU WILD-TYPE                        28   363
D86V14, multiclass
                                  clus
vv                                 PTPRU MUTATED PTPRU WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V15, binary
                 cls
clus                0   1
  PTPRU MUTATED     0  13
  PTPRU WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED      0   13
  PTPRU WILD-TYPE    6  336
                        clus
vv                       PTPRU MUTATED PTPRU WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(87) Variable = ADAM10 MUTATION ANALYSIS
D87V1, survival
                  sevent
clus2                0   1
  ADAM10 MUTATED     6   1
  ADAM10 WILD-TYPE 309 140
  ADAM10 MUTATED ADAM10 WILD-TYPE 
               7              449 
  ADAM10 MUTATED ADAM10 WILD-TYPE 
               1              140 
$`ADAM10 MUTATED`
TCGA-44-8120 TCGA-50-5932 TCGA-55-A490 TCGA-67-3771 TCGA-86-8279 TCGA-NJ-A4YF 
        8.55        40.60         1.58        20.05        15.85        71.05 
TCGA-NJ-A55R 
       19.82 

$`ADAM10 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       15.75        16.08        15.65        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        59.11 

  ADAM10 MUTATED ADAM10 WILD-TYPE 
            1.58             0.00 
  ADAM10 MUTATED ADAM10 WILD-TYPE 
           71.05           223.96 
  ADAM10 MUTATED ADAM10 WILD-TYPE 
           19.82            17.98 
[1] "1.6 - 71.0 (19.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.4"
D87V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADAM10 MUTATED         0        3        1         2         1          1
  ADAM10 WILD-TYPE       4      120      132        44        66         69
                  vv
clus               STAGE IIIB STAGE IV
  ADAM10 MUTATED            0        0
  ADAM10 WILD-TYPE         11       25
D87V3, multiclass
            clus
vv           ADAM10 MUTATED ADAM10 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                1              132
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM10 MUTATED     3   5   0   0
  ADAM10 WILD-TYPE 152 256  43  18
D87V4, multiclass
    clus
vv   ADAM10 MUTATED ADAM10 WILD-TYPE
  T1              3              152
  T2              5              256
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ADAM10 MUTATED     5   2     1
  ADAM10 WILD-TYPE 302  87    71
D87V5, multiclass
       clus
vv      ADAM10 MUTATED ADAM10 WILD-TYPE
  N0                 5              302
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  ADAM10 MUTATED     6   0
  ADAM10 WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM10 MUTATED      6    0
  ADAM10 WILD-TYPE  321   23
   clus
vv  ADAM10 MUTATED ADAM10 WILD-TYPE
  0              6              321
  1              0               23
[1] 2 2
[1] FALSE
D87V7, binary
                  cls
clus                 0   1
  ADAM10 MUTATED     3   5
  ADAM10 WILD-TYPE 256 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM10 MUTATED      3    5
  ADAM10 WILD-TYPE  256  216
        clus
vv       ADAM10 MUTATED ADAM10 WILD-TYPE
  FEMALE              3              256
  MALE                5              216
[1] 2 2
[1] FALSE
D87V8, continuous
[1] "Remove cluster labels:" "ADAM10 MUTATED"        
clus
  ADAM10 MUTATED ADAM10 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"ADAM10 WILD-TYPE" "ADAM10 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADAM10 MUTATED                            0                                 1
  ADAM10 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADAM10 MUTATED                                                    7
  ADAM10 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADAM10 MUTATED                                            0
  ADAM10 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADAM10 MUTATED                                               0
  ADAM10 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ADAM10 MUTATED                                0
  ADAM10 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ADAM10 MUTATED                                    0
  ADAM10 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADAM10 MUTATED                              0                             0
  ADAM10 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADAM10 MUTATED                                               0
  ADAM10 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ADAM10 MUTATED                              0
  ADAM10 WILD-TYPE                            9
D87V9, multiclass
                                                    clus
vv                                                   ADAM10 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ADAM10 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V10, binary
                  cls
clus                 0   1
  ADAM10 MUTATED     0   8
  ADAM10 WILD-TYPE  20 452
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM10 MUTATED      0    8
  ADAM10 WILD-TYPE   20  452
     clus
vv    ADAM10 MUTATED ADAM10 WILD-TYPE
  NO               0               20
  YES              8              452
[1] 2 2
[1] FALSE
D87V11, continuous
D87V12, continuous
                  vv
clus                R0  R1  R2  RX
  ADAM10 MUTATED     4   0   0   0
  ADAM10 WILD-TYPE 306  11   4  25
D87V13, multiclass
    clus
vv   ADAM10 MUTATED ADAM10 WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM10 MUTATED                                  0     0
  ADAM10 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM10 MUTATED                           3     4
  ADAM10 WILD-TYPE                        26   373
D87V14, multiclass
                                  clus
vv                                 ADAM10 MUTATED ADAM10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                         4              373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V15, binary
                  cls
clus                 0   1
  ADAM10 MUTATED     0   7
  ADAM10 WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM10 MUTATED      0    7
  ADAM10 WILD-TYPE    6  342
                        clus
vv                       ADAM10 MUTATED ADAM10 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(88) Variable = MRPS35 MUTATION ANALYSIS
D88V1, survival
                  sevent
clus2                0   1
  MRPS35 MUTATED     4   2
  MRPS35 WILD-TYPE 311 139
  MRPS35 MUTATED MRPS35 WILD-TYPE 
               6              450 
  MRPS35 MUTATED MRPS35 WILD-TYPE 
               2              139 
$`MRPS35 MUTATED`
TCGA-38-4625 TCGA-44-7661 TCGA-44-7670 TCGA-50-8460 TCGA-55-A4DF TCGA-78-7155 
       97.74        12.03        29.00        27.25        20.19        38.50 

$`MRPS35 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        14.60        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
        1.58        20.58        19.59         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MRPS35 MUTATED MRPS35 WILD-TYPE 
           12.03             0.00 
  MRPS35 MUTATED MRPS35 WILD-TYPE 
           97.74           223.96 
  MRPS35 MUTATED MRPS35 WILD-TYPE 
          28.125           17.835 
[1] "12.0 - 97.7 (28.1)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.6"
D88V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MRPS35 MUTATED         0        2        3         1         0          0
  MRPS35 WILD-TYPE       4      121      130        45        67         70
                  vv
clus               STAGE IIIB STAGE IV
  MRPS35 MUTATED            0        0
  MRPS35 WILD-TYPE         11       25
D88V3, multiclass
            clus
vv           MRPS35 MUTATED MRPS35 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                3              130
  STAGE IIA               1               45
  STAGE IIB               0               67
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPS35 MUTATED     3   3   0   0
  MRPS35 WILD-TYPE 152 258  43  18
D88V4, multiclass
    clus
vv   MRPS35 MUTATED MRPS35 WILD-TYPE
  T1              3              152
  T2              3              258
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  MRPS35 MUTATED     5   1     0
  MRPS35 WILD-TYPE 302  88    72
D88V5, multiclass
       clus
vv      MRPS35 MUTATED MRPS35 WILD-TYPE
  N0                 5              302
  N1                 1               88
  N2+N3              0               72
[1] 3 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
  MRPS35 MUTATED     5   0
  MRPS35 WILD-TYPE 322  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS35 MUTATED      5    0
  MRPS35 WILD-TYPE  322   23
   clus
vv  MRPS35 MUTATED MRPS35 WILD-TYPE
  0              5              322
  1              0               23
[1] 2 2
[1] FALSE
D88V7, binary
                  cls
clus                 0   1
  MRPS35 MUTATED     3   3
  MRPS35 WILD-TYPE 256 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS35 MUTATED      3    3
  MRPS35 WILD-TYPE  256  218
        clus
vv       MRPS35 MUTATED MRPS35 WILD-TYPE
  FEMALE              3              256
  MALE                3              218
[1] 2 2
[1] FALSE
D88V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MRPS35 MUTATED                            0                                 0
  MRPS35 WILD-TYPE                         18                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MRPS35 MUTATED                                                    5
  MRPS35 WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MRPS35 MUTATED                                            0
  MRPS35 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MRPS35 MUTATED                                               0
  MRPS35 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  MRPS35 MUTATED                                0
  MRPS35 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  MRPS35 MUTATED                                    0
  MRPS35 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MRPS35 MUTATED                              0                             1
  MRPS35 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MRPS35 MUTATED                                               0
  MRPS35 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  MRPS35 MUTATED                              0
  MRPS35 WILD-TYPE                            9
D88V9, multiclass
                                                    clus
vv                                                   MRPS35 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   MRPS35 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V10, binary
                  cls
clus                 0   1
  MRPS35 MUTATED     0   6
  MRPS35 WILD-TYPE  20 454
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS35 MUTATED      0    6
  MRPS35 WILD-TYPE   20  454
     clus
vv    MRPS35 MUTATED MRPS35 WILD-TYPE
  NO               0               20
  YES              6              454
[1] 2 2
[1] FALSE
D88V11, continuous
D88V12, continuous
                  vv
clus                R0  R1  R2  RX
  MRPS35 MUTATED     4   0   0   0
  MRPS35 WILD-TYPE 306  11   4  25
D88V13, multiclass
    clus
vv   MRPS35 MUTATED MRPS35 WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPS35 MUTATED                                  0     0
  MRPS35 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPS35 MUTATED                           0     6
  MRPS35 WILD-TYPE                        29   371
D88V14, multiclass
                                  clus
vv                                 MRPS35 MUTATED MRPS35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         6              371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V15, binary
                  cls
clus                 0   1
  MRPS35 MUTATED     1   4
  MRPS35 WILD-TYPE   5 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS35 MUTATED      1    4
  MRPS35 WILD-TYPE    5  345
                        clus
vv                       MRPS35 MUTATED MRPS35 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(89) Variable = ZNF608 MUTATION ANALYSIS
D89V1, survival
                  sevent
clus2                0   1
  ZNF608 MUTATED     5   4
  ZNF608 WILD-TYPE 310 137
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              447 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               4              137 
$`ZNF608 MUTATED`
TCGA-05-4415 TCGA-44-7667 TCGA-55-8203 TCGA-55-8299 TCGA-86-8054 TCGA-91-6831 
        2.99        36.07        17.98        15.42        24.49        10.19 
TCGA-91-8497 TCGA-95-7562 TCGA-97-A4M5 
       14.27         2.86        20.84 

$`ZNF608 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        22.16         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       16.70         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC 
        7.36         1.15        16.18        16.60         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         1.22        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 
       20.19        21.44        19.76        20.52        17.75        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ZNF608 MUTATED ZNF608 WILD-TYPE 
            2.86             0.00 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           36.07           223.96 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           15.42            18.12 
[1] "2.9 - 36.1 (15.4)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.4"
D89V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF608 MUTATED         0        3        2         1         2          0
  ZNF608 WILD-TYPE       4      120      131        45        65         70
                  vv
clus               STAGE IIIB STAGE IV
  ZNF608 MUTATED            1        0
  ZNF608 WILD-TYPE         10       25
D89V3, multiclass
            clus
vv           ZNF608 MUTATED ZNF608 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                2              131
  STAGE IIA               1               45
  STAGE IIB               2               65
  STAGE IIIA              0               70
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF608 MUTATED     4   3   1   1
  ZNF608 WILD-TYPE 151 258  42  17
D89V4, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  T1              4              151
  T2              3              258
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  ZNF608 MUTATED     6   2     1
  ZNF608 WILD-TYPE 301  87    71
D89V5, multiclass
       clus
vv      ZNF608 MUTATED ZNF608 WILD-TYPE
  N0                 6              301
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  ZNF608 MUTATED     4   0
  ZNF608 WILD-TYPE 323  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      4    0
  ZNF608 WILD-TYPE  323   23
   clus
vv  ZNF608 MUTATED ZNF608 WILD-TYPE
  0              4              323
  1              0               23
[1] 2 2
[1] FALSE
D89V7, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     4   5
  ZNF608 WILD-TYPE 255 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      4    5
  ZNF608 WILD-TYPE  255  216
        clus
vv       ZNF608 MUTATED ZNF608 WILD-TYPE
  FEMALE              4              255
  MALE                5              216
[1] 2 2
[1] FALSE
D89V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF608 MUTATED                            1                                 2
  ZNF608 WILD-TYPE                         17                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF608 MUTATED                                                    6
  ZNF608 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF608 MUTATED                                            0
  ZNF608 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF608 MUTATED                                               0
  ZNF608 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF608 MUTATED                                0
  ZNF608 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF608 MUTATED                                    0
  ZNF608 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF608 MUTATED                              0                             0
  ZNF608 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF608 MUTATED                                               0
  ZNF608 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF608 MUTATED                              0
  ZNF608 WILD-TYPE                            9
D89V9, multiclass
                                                    clus
vv                                                   ZNF608 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF608 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V10, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     0   9
  ZNF608 WILD-TYPE  20 451
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      0    9
  ZNF608 WILD-TYPE   20  451
     clus
vv    ZNF608 MUTATED ZNF608 WILD-TYPE
  NO               0               20
  YES              9              451
[1] 2 2
[1] FALSE
D89V11, continuous
D89V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF608 MUTATED     4   0   0   1
  ZNF608 WILD-TYPE 306  11   4  24
D89V13, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF608 MUTATED                                  0     0
  ZNF608 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF608 MUTATED                           1     7
  ZNF608 WILD-TYPE                        28   370
D89V14, multiclass
                                  clus
vv                                 ZNF608 MUTATED ZNF608 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V15, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     0   8
  ZNF608 WILD-TYPE   6 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      0    8
  ZNF608 WILD-TYPE    6  341
                        clus
vv                       ZNF608 MUTATED ZNF608 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              341
[1] 2 2
[1] FALSE

Clustering(90) Variable = ARHGAP32 MUTATION ANALYSIS
D90V1, survival
                    sevent
clus2                  0   1
  ARHGAP32 MUTATED    11   6
  ARHGAP32 WILD-TYPE 304 135
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                17                439 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                 6                135 
$`ARHGAP32 MUTATED`
TCGA-05-4382 TCGA-44-3918 TCGA-44-4112 TCGA-44-5644 TCGA-44-7667 TCGA-50-5932 
       19.96        34.06        26.56        28.37        36.07        40.60 
TCGA-55-8096 TCGA-55-8507 TCGA-78-7155 TCGA-78-8640 TCGA-78-8662 TCGA-86-8073 
       23.64         0.26        38.50       214.62       110.50        24.33 
TCGA-86-A4JF TCGA-93-A4JQ TCGA-95-7562 TCGA-97-A4M3 TCGA-99-8025 
       17.62        17.29         2.86        17.75        34.85 

$`ARHGAP32 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-5643 TCGA-44-5645 
       42.77        37.15        38.24         6.25        33.30        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03         7.17        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        8.22         9.27        14.27        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       19.00         1.12         1.22        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
              0.26               0.00 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
            214.62             223.96 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
             26.56              17.65 
[1] "0.3 - 214.6 (26.6)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.5"
D90V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARHGAP32 MUTATED         0        5        8         2         3          1
  ARHGAP32 WILD-TYPE       4      118      125        44        64         69
                    vv
clus                 STAGE IIIB STAGE IV
  ARHGAP32 MUTATED            0        0
  ARHGAP32 WILD-TYPE         11       25
D90V3, multiclass
            clus
vv           ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  5                118
  STAGE IB                  8                125
  STAGE IIA                 2                 44
  STAGE IIB                 3                 64
  STAGE IIIA                1                 69
  STAGE IIIB                0                 11
  STAGE IV                  0                 25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP32 MUTATED     6  10   3   0
  ARHGAP32 WILD-TYPE 149 251  40  18
D90V4, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  T1                6                149
  T2               10                251
  T3                3                 40
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  ARHGAP32 MUTATED    15   3     1
  ARHGAP32 WILD-TYPE 292  86    71
D90V5, multiclass
       clus
vv      ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  N0                  15                292
  N1                   3                 86
  N2+N3                1                 71
[1] 3 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
  ARHGAP32 MUTATED    14   0
  ARHGAP32 WILD-TYPE 313  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     14    0
  ARHGAP32 WILD-TYPE  313   23
   clus
vv  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  0               14                313
  1                0                 23
[1] 2 2
[1] FALSE
D90V7, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED     9  10
  ARHGAP32 WILD-TYPE 250 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED      9   10
  ARHGAP32 WILD-TYPE  250  211
        clus
vv       ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  FEMALE                9                250
  MALE                 10                211
[1] 2 2
[1] FALSE
D90V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  ARHGAP32 MUTATED                            1
  ARHGAP32 WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARHGAP32 MUTATED                                   2
  ARHGAP32 WILD-TYPE                               100
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP32 MUTATED                                                   15
  ARHGAP32 WILD-TYPE                                                279
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARHGAP32 MUTATED                                            0
  ARHGAP32 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARHGAP32 MUTATED                                               1
  ARHGAP32 WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  ARHGAP32 MUTATED                                0
  ARHGAP32 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  ARHGAP32 MUTATED                                    0
  ARHGAP32 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARHGAP32 MUTATED                              0                             0
  ARHGAP32 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARHGAP32 MUTATED                                               0
  ARHGAP32 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  ARHGAP32 MUTATED                              0
  ARHGAP32 WILD-TYPE                            9
D90V9, multiclass
                                                    clus
vv                                                   ARHGAP32 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   ARHGAP32 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V10, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED     0  19
  ARHGAP32 WILD-TYPE  20 441
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED      0   19
  ARHGAP32 WILD-TYPE   20  441
     clus
vv    ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  NO                 0                 20
  YES               19                441
[1] 2 2
[1] FALSE
D90V11, continuous
D90V12, continuous
                    vv
clus                  R0  R1  R2  RX
  ARHGAP32 MUTATED    12   0   0   2
  ARHGAP32 WILD-TYPE 298  11   4  23
D90V13, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  R0               12                298
  R1                0                 11
  R2                0                  4
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP32 MUTATED                                  0     0
  ARHGAP32 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP32 MUTATED                           2    12
  ARHGAP32 WILD-TYPE                        27   365
D90V14, multiclass
                                  clus
vv                                 ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       2                 27
  WHITE                                          12                365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V15, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED     0  13
  ARHGAP32 WILD-TYPE   6 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED      0   13
  ARHGAP32 WILD-TYPE    6  336
                        clus
vv                       ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               13                336
[1] 2 2
[1] FALSE

Clustering(91) Variable = NRAS MUTATION ANALYSIS
D91V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     2   1
  NRAS WILD-TYPE 313 140
  NRAS MUTATED NRAS WILD-TYPE 
             3            453 
  NRAS MUTATED NRAS WILD-TYPE 
             1            140 
$`NRAS MUTATED`
TCGA-35-4123 TCGA-38-4632 TCGA-69-7979 
        5.98        44.61         2.93 

$`NRAS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  NRAS MUTATED NRAS WILD-TYPE 
          2.93           0.00 
  NRAS MUTATED NRAS WILD-TYPE 
         44.61         223.96 
  NRAS MUTATED NRAS WILD-TYPE 
          5.98          18.08 
[1] "2.9 - 44.6 (6.0)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D91V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NRAS MUTATED         0        1        1         0         0          0
  NRAS WILD-TYPE       4      122      132        46        67         70
                vv
clus             STAGE IIIB STAGE IV
  NRAS MUTATED            0        1
  NRAS WILD-TYPE         11       24
D91V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              1            132
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRAS MUTATED     1   2   0   0
  NRAS WILD-TYPE 154 259  43  18
D91V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            1            154
  T2            2            259
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  NRAS MUTATED     2   1     0
  NRAS WILD-TYPE 305  88    72
D91V5, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  N0               2            305
  N1               1             88
  N2+N3            0             72
[1] 3 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
  NRAS MUTATED     1   1
  NRAS WILD-TYPE 326  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    1
  NRAS WILD-TYPE  326   22
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            1            326
  1            1             22
[1] 2 2
[1] FALSE
D91V7, binary
                cls
clus               0   1
  NRAS MUTATED     1   2
  NRAS WILD-TYPE 258 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    2
  NRAS WILD-TYPE  258  219
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            1            258
  MALE              2            219
[1] 2 2
[1] FALSE
D91V8, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-5375     TCGA-53-A4EZ     TCGA-55-7283 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7573     TCGA-55-7725     TCGA-55-7910     TCGA-55-7914 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NRAS MUTATED                            1                                 0
  NRAS WILD-TYPE                         17                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NRAS MUTATED                                                    2
  NRAS WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NRAS MUTATED                                            0
  NRAS WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NRAS MUTATED                                               0
  NRAS WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  NRAS MUTATED                                0
  NRAS WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  NRAS MUTATED                                    0
  NRAS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NRAS MUTATED                              0                             0
  NRAS WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NRAS MUTATED                                               0
  NRAS WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  NRAS MUTATED                              0
  NRAS WILD-TYPE                            9
D91V9, multiclass
                                                    clus
vv                                                   NRAS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   NRAS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V10, binary
                cls
clus               0   1
  NRAS MUTATED     0   3
  NRAS WILD-TYPE  20 457
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    3
  NRAS WILD-TYPE   20  457
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             0             20
  YES            3            457
[1] 2 2
[1] FALSE
D91V11, continuous
D91V12, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-5375 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-7271     TCGA-38-A44F 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-3396     TCGA-44-3398 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-5644     TCGA-44-5645 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6147     TCGA-44-6148 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4494     TCGA-49-4505     TCGA-53-7624 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-1592 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-1595     TCGA-55-5899     TCGA-55-6642     TCGA-55-6712 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6971     TCGA-55-7227     TCGA-55-7283     TCGA-55-7570 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7728     TCGA-55-7907     TCGA-55-7910 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7914     TCGA-55-8089     TCGA-55-8092 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8205 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8506 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8511     TCGA-55-8512     TCGA-55-8514 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-62-8398 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5774     TCGA-64-5775 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5779     TCGA-64-5781     TCGA-69-7761 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-69-7763     TCGA-69-7764     TCGA-69-7765     TCGA-69-7974 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K     TCGA-73-4659 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-7498     TCGA-75-6214 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-7025     TCGA-75-7027     TCGA-75-7031     TCGA-78-7145 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7542 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6851     TCGA-86-7711     TCGA-86-7714 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7954     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6836 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED     2   0   0   0
  NRAS WILD-TYPE 308  11   4  25
D91V13, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            348 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-5375 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-4627     TCGA-38-4628 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4629     TCGA-38-4630     TCGA-38-4631     TCGA-38-6178 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-7271     TCGA-38-A44F     TCGA-44-2657     TCGA-44-2661 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-2665     TCGA-44-3396     TCGA-44-3398     TCGA-44-3918 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-3919     TCGA-44-4112     TCGA-44-6144     TCGA-44-6148 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4487 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4488     TCGA-49-4494     TCGA-49-4501     TCGA-49-4505 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4507     TCGA-49-4510     TCGA-49-4512 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4514     TCGA-49-6742     TCGA-49-6744     TCGA-49-6761 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-6767     TCGA-50-5051     TCGA-50-5055     TCGA-50-5066 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-50-6597     TCGA-50-6673     TCGA-50-8460     TCGA-53-7624 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-1592     TCGA-55-5899 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6970     TCGA-55-6971     TCGA-55-6972 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6980     TCGA-55-6981     TCGA-55-6983     TCGA-55-6985 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7281     TCGA-55-7284     TCGA-55-7570     TCGA-55-7574 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7576     TCGA-55-7724     TCGA-55-7725     TCGA-55-7726 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7727     TCGA-55-7728     TCGA-55-7815     TCGA-55-7903 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8085     TCGA-55-8087 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8090     TCGA-55-8091     TCGA-55-8092 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8203     TCGA-55-8204 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8206     TCGA-55-8207     TCGA-55-8208 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8505 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8508     TCGA-55-8510 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8513     TCGA-55-8514 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8614     TCGA-55-8615     TCGA-55-8616     TCGA-55-8619 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-1676     TCGA-64-1677     TCGA-64-1679     TCGA-64-1681 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5781     TCGA-64-5815     TCGA-67-3771     TCGA-67-3773 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-67-4679     TCGA-67-6215     TCGA-67-6216     TCGA-67-6217 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4658     TCGA-73-4659 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-7499     TCGA-75-5122     TCGA-75-5125     TCGA-75-5126 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-5146     TCGA-75-5147     TCGA-75-6203     TCGA-75-6205 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-6206     TCGA-75-6207     TCGA-75-6211     TCGA-75-6212 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7030 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7143     TCGA-78-7145     TCGA-78-7146 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7147     TCGA-78-7148     TCGA-78-7149     TCGA-78-7150 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7152     TCGA-78-7153     TCGA-78-7154     TCGA-78-7155 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7156     TCGA-78-7158     TCGA-78-7159     TCGA-78-7160 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7166 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7167     TCGA-78-7220     TCGA-78-7535     TCGA-78-7536 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7537     TCGA-78-7539     TCGA-78-7540     TCGA-78-7542 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-80-5611     TCGA-83-5908     TCGA-86-6562     TCGA-86-7701 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7711     TCGA-86-7713     TCGA-86-7714     TCGA-86-7953 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8054     TCGA-86-8055 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8585     TCGA-86-8668 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-8672     TCGA-86-8673 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6828     TCGA-91-6829     TCGA-91-6835     TCGA-91-6840 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-7546 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-7554     TCGA-97-7938     TCGA-97-7941     TCGA-97-8176 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-99-8028     TCGA-99-8032     TCGA-99-8033     TCGA-J2-A4AD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAS MUTATED                                  0     0
  NRAS WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED                           1     2
  NRAS WILD-TYPE                        28   375
D91V14, multiclass
                                  clus
vv                                 NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       2            375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V15, binary
                cls
clus               0   1
  NRAS MUTATED     0   3
  NRAS WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    3
  NRAS WILD-TYPE    6  346
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(92) Variable = HCLS1 MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2               0   1
  HCLS1 MUTATED     8   7
  HCLS1 WILD-TYPE 307 134
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             15             441 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
              7             134 
$`HCLS1 MUTATED`
TCGA-49-4505 TCGA-49-4514 TCGA-50-5072 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-A490 
       14.07        55.89         8.22        30.54         9.21         1.58 
TCGA-67-6217 TCGA-69-7978 TCGA-78-7146 TCGA-78-7150 TCGA-86-6851 TCGA-95-A4VK 
       13.87         2.30         5.69        21.90         5.88        21.40 
TCGA-97-8174 TCGA-NJ-A4YI TCGA-NJ-A55A 
        5.39         0.13         0.26 

$`HCLS1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        46.72        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.46        29.75        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 
        7.59        27.25        34.29        13.94        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
        2.17        16.93        22.65        20.71        21.40        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       39.09        23.51       163.10        27.16        19.27        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       35.93        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05        62.60         1.64        29.13 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  HCLS1 MUTATED HCLS1 WILD-TYPE 
           0.13            0.00 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
          55.89          223.96 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
           8.22           18.64 
[1] "0.1 - 55.9 (8.2)"   "0.0 - 224.0 (18.6)"
[1] "hr=" "2.9"
D92V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HCLS1 MUTATED         0        1        1         6         3          5
  HCLS1 WILD-TYPE       4      122      132        40        64         65
                 vv
clus              STAGE IIIB STAGE IV
  HCLS1 MUTATED            0        0
  HCLS1 WILD-TYPE         11       25
D92V3, multiclass
            clus
vv           HCLS1 MUTATED HCLS1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               1             132
  STAGE IIA              6              40
  STAGE IIB              3              64
  STAGE IIIA             5              65
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HCLS1 MUTATED     3  12   1   0
  HCLS1 WILD-TYPE 152 249  42  18
D92V4, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  T1             3             152
  T2            12             249
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  HCLS1 MUTATED     4   7     5
  HCLS1 WILD-TYPE 303  82    67
D92V5, multiclass
       clus
vv      HCLS1 MUTATED HCLS1 WILD-TYPE
  N0                4             303
  N1                7              82
  N2+N3             5              67
[1] 3 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
  HCLS1 MUTATED    13   0
  HCLS1 WILD-TYPE 314  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     13    0
  HCLS1 WILD-TYPE  314   23
   clus
vv  HCLS1 MUTATED HCLS1 WILD-TYPE
  0            13             314
  1             0              23
[1] 2 2
[1] FALSE
D92V7, binary
                 cls
clus                0   1
  HCLS1 MUTATED    10   6
  HCLS1 WILD-TYPE 249 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     10    6
  HCLS1 WILD-TYPE  249  215
        clus
vv       HCLS1 MUTATED HCLS1 WILD-TYPE
  FEMALE            10             249
  MALE               6             215
[1] 2 2
[1] FALSE
D92V8, continuous
[1] "Remove cluster labels:" "HCLS1 MUTATED"         
clus
  HCLS1 MUTATED HCLS1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-55-7283 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A494 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"HCLS1 WILD-TYPE" "HCLS1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HCLS1 MUTATED                            1                                 4
  HCLS1 WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HCLS1 MUTATED                                                    7
  HCLS1 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HCLS1 MUTATED                                            0
  HCLS1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HCLS1 MUTATED                                               0
  HCLS1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HCLS1 MUTATED                                0
  HCLS1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HCLS1 MUTATED                                    0
  HCLS1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HCLS1 MUTATED                              0                             4
  HCLS1 WILD-TYPE                            2                            18
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HCLS1 MUTATED                                               0
  HCLS1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HCLS1 MUTATED                              0
  HCLS1 WILD-TYPE                            9
D92V9, multiclass
                                                    clus
vv                                                   HCLS1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HCLS1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   18
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V10, binary
                 cls
clus                0   1
  HCLS1 MUTATED     1  15
  HCLS1 WILD-TYPE  19 445
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED      1   15
  HCLS1 WILD-TYPE   19  445
     clus
vv    HCLS1 MUTATED HCLS1 WILD-TYPE
  NO              1              19
  YES            15             445
[1] 2 2
[1] FALSE
D92V11, continuous
D92V12, continuous
                 vv
clus               R0  R1  R2  RX
  HCLS1 MUTATED     7   0   1   2
  HCLS1 WILD-TYPE 303  11   3  23
D92V13, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             1               3
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCLS1 MUTATED                                  0     0
  HCLS1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HCLS1 MUTATED                           0    15
  HCLS1 WILD-TYPE                        29   362
D92V14, multiclass
                                  clus
vv                                 HCLS1 MUTATED HCLS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       15             362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V15, binary
                 cls
clus                0   1
  HCLS1 MUTATED     1  10
  HCLS1 WILD-TYPE   5 339
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED      1   10
  HCLS1 WILD-TYPE    5  339
                        clus
vv                       HCLS1 MUTATED HCLS1 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            10             339
[1] 2 2
[1] FALSE

Clustering(93) Variable = KIAA0895L MUTATION ANALYSIS
D93V1, survival
                     sevent
clus2                   0   1
  KIAA0895L MUTATED     2   2
  KIAA0895L WILD-TYPE 313 139
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
                  4                 452 
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
                  2                 139 
$`KIAA0895L MUTATED`
TCGA-55-8092 TCGA-62-8402 TCGA-69-7979 TCGA-NJ-A4YF 
        5.06        49.25         2.93        71.05 

$`KIAA0895L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.66        19.73         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
               2.93                0.00 
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
              71.05              223.96 
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
             27.155              18.030 
[1] "2.9 - 71.0 (27.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1"  
D93V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KIAA0895L MUTATED         0        1        1         0         1          1
  KIAA0895L WILD-TYPE       4      122      132        46        66         69
                     vv
clus                  STAGE IIIB STAGE IV
  KIAA0895L MUTATED            0        0
  KIAA0895L WILD-TYPE         11       25
D93V3, multiclass
            clus
vv           KIAA0895L MUTATED KIAA0895L WILD-TYPE
  STAGE I                    0                   4
  STAGE IA                   1                 122
  STAGE IB                   1                 132
  STAGE IIA                  0                  46
  STAGE IIB                  1                  66
  STAGE IIIA                 1                  69
  STAGE IIIB                 0                  11
  STAGE IV                   0                  25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KIAA0895L MUTATED     1   2   1   0
  KIAA0895L WILD-TYPE 154 259  42  18
D93V4, multiclass
    clus
vv   KIAA0895L MUTATED KIAA0895L WILD-TYPE
  T1                 1                 154
  T2                 2                 259
  T3                 1                  42
  T4                 0                  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"
                     vv
clus                   N0  N1 N2+N3
  KIAA0895L MUTATED     3   0     1
  KIAA0895L WILD-TYPE 304  89    71
D93V5, multiclass
       clus
vv      KIAA0895L MUTATED KIAA0895L WILD-TYPE
  N0                    3                 304
  N1                    0                  89
  N2+N3                 1                  71
[1] 3 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
  KIAA0895L MUTATED     2   0
  KIAA0895L WILD-TYPE 325  23
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0895L MUTATED      2    0
  KIAA0895L WILD-TYPE  325   23
   clus
vv  KIAA0895L MUTATED KIAA0895L WILD-TYPE
  0                 2                 325
  1                 0                  23
[1] 2 2
[1] FALSE
D93V7, binary
                     cls
clus                    0   1
  KIAA0895L MUTATED     3   1
  KIAA0895L WILD-TYPE 256 220
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0895L MUTATED      3    1
  KIAA0895L WILD-TYPE  256  220
        clus
vv       KIAA0895L MUTATED KIAA0895L WILD-TYPE
  FEMALE                 3                 256
  MALE                   1                 220
[1] 2 2
[1] FALSE
D93V8, continuous
[1] "Remove cluster labels:" "KIAA0895L MUTATED"     
clus
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
                  1                  83 
         TCGA-35-4122          TCGA-35-4123          TCGA-35-5375 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-53-A4EZ          TCGA-55-7283          TCGA-55-7573 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7725          TCGA-55-7910          TCGA-55-7914 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8089          TCGA-55-8096          TCGA-55-8205 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8208          TCGA-55-8507          TCGA-55-8508 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8511          TCGA-55-8512          TCGA-55-8619 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8620          TCGA-55-A48Z          TCGA-55-A490 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-A494          TCGA-62-8394          TCGA-62-8395 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-8397          TCGA-62-8398          TCGA-62-8399 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-A46O          TCGA-62-A46P          TCGA-62-A46R 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-A46S          TCGA-62-A46U          TCGA-62-A46V 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-A46Y          TCGA-62-A470          TCGA-62-A471 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-A472          TCGA-64-1677          TCGA-64-1681 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-64-5778          TCGA-69-7974          TCGA-69-8254 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-71-6725          TCGA-71-8520          TCGA-73-4659 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4662          TCGA-73-4666          TCGA-73-4668 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4676          TCGA-73-7498          TCGA-73-7499 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-75-5122          TCGA-83-5908          TCGA-86-7701 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-7711          TCGA-86-7713          TCGA-86-7714 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-7954          TCGA-86-7955          TCGA-86-8055 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8056          TCGA-86-8074          TCGA-86-8075 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8076          TCGA-86-8278          TCGA-86-8279 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8281          TCGA-86-8358          TCGA-86-8359 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8668          TCGA-86-8669          TCGA-86-8671 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-A4JF          TCGA-86-A4P7          TCGA-91-6849 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-93-7348          TCGA-93-8067          TCGA-93-A4JN 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-93-A4JO          TCGA-99-7458          TCGA-MN-A4N1 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MN-A4N4          TCGA-MN-A4N5 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
                     vv
clus                  LUNG ACINAR ADENOCARCINOMA
  KIAA0895L MUTATED                            1
  KIAA0895L WILD-TYPE                         17
                     vv
clus                  LUNG ADENOCARCINOMA MIXED SUBTYPE
  KIAA0895L MUTATED                                   2
  KIAA0895L WILD-TYPE                               100
                     vv
clus                  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KIAA0895L MUTATED                                                    1
  KIAA0895L WILD-TYPE                                                293
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KIAA0895L MUTATED                                            0
  KIAA0895L WILD-TYPE                                          4
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KIAA0895L MUTATED                                               0
  KIAA0895L WILD-TYPE                                            19
                     vv
clus                  LUNG CLEAR CELL ADENOCARCINOMA
  KIAA0895L MUTATED                                0
  KIAA0895L WILD-TYPE                              2
                     vv
clus                  LUNG MICROPAPILLARY ADENOCARCINOMA
  KIAA0895L MUTATED                                    0
  KIAA0895L WILD-TYPE                                  3
                     vv
clus                  LUNG MUCINOUS ADENOCARCINOMA
  KIAA0895L MUTATED                              0
  KIAA0895L WILD-TYPE                            2
                     vv
clus                  LUNG PAPILLARY ADENOCARCINOMA
  KIAA0895L MUTATED                               0
  KIAA0895L WILD-TYPE                            22
                     vv
clus                  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KIAA0895L MUTATED                                               0
  KIAA0895L WILD-TYPE                                             5
                     vv
clus                  MUCINOUS (COLLOID) CARCINOMA
  KIAA0895L MUTATED                              0
  KIAA0895L WILD-TYPE                            9
D93V9, multiclass
                                                    clus
vv                                                   KIAA0895L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                         1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      0
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       0
  LUNG PAPILLARY ADENOCARCINOMA                                      0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      0
  MUCINOUS (COLLOID) CARCINOMA                                       0
                                                    clus
vv                                                   KIAA0895L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                           4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                       19
  LUNG CLEAR CELL ADENOCARCINOMA                                       2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                   3
  LUNG MUCINOUS ADENOCARCINOMA                                         2
  LUNG PAPILLARY ADENOCARCINOMA                                       22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                        5
  MUCINOUS (COLLOID) CARCINOMA                                         9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V10, binary
                     cls
clus                    0   1
  KIAA0895L MUTATED     0   4
  KIAA0895L WILD-TYPE  20 456
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0895L MUTATED      0    4
  KIAA0895L WILD-TYPE   20  456
     clus
vv    KIAA0895L MUTATED KIAA0895L WILD-TYPE
  NO                  0                  20
  YES                 4                 456
[1] 2 2
[1] FALSE
D93V11, continuous
D93V12, continuous
[1] "Remove cluster labels:" "KIAA0895L MUTATED"     
clus
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
                  2                 255 
         TCGA-05-4384          TCGA-05-4390          TCGA-05-4396 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4405          TCGA-05-4410          TCGA-05-4415 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4417          TCGA-05-4424          TCGA-05-4427 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4433          TCGA-05-5420          TCGA-05-5423 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-5425          TCGA-05-5428          TCGA-35-4122 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-35-4123          TCGA-35-5375          TCGA-38-4625 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-38-4626          TCGA-38-7271          TCGA-38-A44F 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-2656          TCGA-44-2657          TCGA-44-3396 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-3398          TCGA-44-3918          TCGA-44-4112 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-5644          TCGA-44-5645          TCGA-44-6144 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-6145          TCGA-44-6147          TCGA-44-6148 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-6774          TCGA-44-6775          TCGA-44-6776 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-6777          TCGA-44-6778          TCGA-44-6779 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-7659          TCGA-44-7660          TCGA-44-7661 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-7662          TCGA-44-7667          TCGA-44-7669 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-7670          TCGA-44-7672          TCGA-44-8117 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-8119          TCGA-44-8120          TCGA-44-A479 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-A47A          TCGA-44-A47B          TCGA-44-A47F 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-A47G          TCGA-44-A4SS          TCGA-44-A4SU 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-49-4486          TCGA-49-4494          TCGA-49-4505 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-53-7624          TCGA-53-7626          TCGA-53-7813 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-53-A4EZ          TCGA-55-1592          TCGA-55-1595 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-5899          TCGA-55-6642          TCGA-55-6712 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-6971          TCGA-55-7227          TCGA-55-7283 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7570          TCGA-55-7574          TCGA-55-7576 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7724          TCGA-55-7725          TCGA-55-7726 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7728          TCGA-55-7907          TCGA-55-7910 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7911          TCGA-55-7914          TCGA-55-8089 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8094          TCGA-55-8096          TCGA-55-8097 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8205          TCGA-55-8299          TCGA-55-8301 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8302          TCGA-55-8506          TCGA-55-8507 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8511          TCGA-55-8512          TCGA-55-8514 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8615          TCGA-55-8620          TCGA-55-8621 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-A48X          TCGA-55-A48Y          TCGA-55-A48Z 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-A490          TCGA-55-A491          TCGA-55-A492 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-A493          TCGA-55-A494          TCGA-62-8398 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-64-1677          TCGA-64-1681          TCGA-64-5774 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-64-5775          TCGA-64-5778          TCGA-64-5779 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-64-5781          TCGA-69-7761          TCGA-69-7763 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-69-7764          TCGA-69-7765          TCGA-69-7974 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-69-8253          TCGA-69-8255          TCGA-69-A59K 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4659          TCGA-73-4662          TCGA-73-4666 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4668          TCGA-73-4670          TCGA-73-4675 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4676          TCGA-73-7498          TCGA-75-6214 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-75-7025          TCGA-75-7027          TCGA-75-7031 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7145          TCGA-78-7146          TCGA-78-7147 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7148          TCGA-78-7149          TCGA-78-7150 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7152          TCGA-78-7153          TCGA-78-7154 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7155          TCGA-78-7156          TCGA-78-7158 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7159          TCGA-78-7160          TCGA-78-7161 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7162          TCGA-78-7163          TCGA-78-7166 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7167          TCGA-78-7220          TCGA-78-7535 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7536          TCGA-78-7537          TCGA-78-7539 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7542          TCGA-78-7633          TCGA-78-8640 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-8648          TCGA-78-8655          TCGA-78-8660 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-8662          TCGA-80-5607          TCGA-80-5608 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-83-5908          TCGA-86-6851          TCGA-86-7711 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-7714          TCGA-86-7954          TCGA-86-8054 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8055          TCGA-86-8056          TCGA-86-8073 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8074          TCGA-86-8281          TCGA-86-8358 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8359          TCGA-86-8669          TCGA-86-8673 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8674          TCGA-86-A456          TCGA-91-6829 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-91-6830          TCGA-91-6836          TCGA-91-6840 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-91-6849          TCGA-91-8499          TCGA-91-A4BC 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-93-7347          TCGA-93-7348          TCGA-93-8067 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-93-A4JN          TCGA-93-A4JO          TCGA-93-A4JQ 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-95-7043          TCGA-95-7562          TCGA-95-7567 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-95-7944          TCGA-95-7947          TCGA-95-7948 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-95-A4VK          TCGA-95-A4VN          TCGA-95-A4VP 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-7546          TCGA-97-7553          TCGA-97-7554 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-7941          TCGA-97-8171          TCGA-97-8172 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-8174          TCGA-97-8176          TCGA-97-8179 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-A4LX          TCGA-97-A4M0          TCGA-97-A4M1 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-A4M2          TCGA-97-A4M3          TCGA-97-A4M5 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-A4M7          TCGA-99-7458          TCGA-99-8025 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-99-8028          TCGA-99-8032          TCGA-J2-8194 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-J2-A4AD          TCGA-J2-A4AG          TCGA-L4-A4E5 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-L4-A4E6          TCGA-L9-A443          TCGA-L9-A444 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MN-A4N1          TCGA-MN-A4N4          TCGA-MN-A4N5 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4SV          TCGA-MP-A4SW          TCGA-MP-A4T2 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4T4          TCGA-MP-A4T7          TCGA-MP-A4T8 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4T9          TCGA-MP-A4TA          TCGA-MP-A4TC 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4TE          TCGA-MP-A4TF          TCGA-MP-A4TH 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4TI          TCGA-MP-A4TK          TCGA-MP-A5C7 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-NJ-A4YG          TCGA-NJ-A4YI          TCGA-O1-A52J 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
                     vv
clus                   R0  R1  R2  RX
  KIAA0895L MUTATED     2   0   0   0
  KIAA0895L WILD-TYPE 308  11   4  25
D93V13, multiclass
[1] "Remove cluster labels:" "KIAA0895L MUTATED"     
clus
  KIAA0895L MUTATED KIAA0895L WILD-TYPE 
                  2                 348 
         TCGA-05-4244          TCGA-05-4249          TCGA-05-4250 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4382          TCGA-05-4384          TCGA-05-4389 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4390          TCGA-05-4395          TCGA-05-4396 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4397          TCGA-05-4398          TCGA-05-4402 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4403          TCGA-05-4405          TCGA-05-4410 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4415          TCGA-05-4417          TCGA-05-4418 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4420          TCGA-05-4422          TCGA-05-4424 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4425          TCGA-05-4426          TCGA-05-4427 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4430          TCGA-05-4432          TCGA-05-4433 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-4434          TCGA-05-5420          TCGA-05-5423 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-5425          TCGA-05-5428          TCGA-05-5429 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-05-5715          TCGA-35-4122          TCGA-35-4123 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-35-5375          TCGA-38-4625          TCGA-38-4626 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-38-4627          TCGA-38-4628          TCGA-38-4629 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-38-4630          TCGA-38-4631          TCGA-38-4632 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-38-6178          TCGA-38-7271          TCGA-38-A44F 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-2657          TCGA-44-2661          TCGA-44-2665 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-3396          TCGA-44-3398          TCGA-44-3918 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-3919          TCGA-44-4112          TCGA-44-6144 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-6148          TCGA-44-6775          TCGA-44-A479 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-A47A          TCGA-44-A47B          TCGA-44-A47G 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-44-A4SU          TCGA-49-4486          TCGA-49-4487 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-49-4488          TCGA-49-4494          TCGA-49-4501 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-49-4505          TCGA-49-4506          TCGA-49-4507 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-49-4510          TCGA-49-4512          TCGA-49-4514 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-49-6742          TCGA-49-6744          TCGA-49-6761 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-49-6767          TCGA-50-5051          TCGA-50-5055 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-50-5066          TCGA-50-5931          TCGA-50-5942 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-50-5944          TCGA-50-6593          TCGA-50-6597 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-50-6673          TCGA-50-8460          TCGA-53-7624 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-53-7626          TCGA-53-A4EZ          TCGA-55-1592 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-5899          TCGA-55-6642          TCGA-55-6970 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-6971          TCGA-55-6972          TCGA-55-6980 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-6981          TCGA-55-6983          TCGA-55-6985 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7281          TCGA-55-7284          TCGA-55-7570 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7574          TCGA-55-7576          TCGA-55-7724 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7725          TCGA-55-7726          TCGA-55-7727 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7728          TCGA-55-7815          TCGA-55-7903 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7907          TCGA-55-7910          TCGA-55-7911 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-7914          TCGA-55-7994          TCGA-55-7995 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8085          TCGA-55-8087          TCGA-55-8089 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8090          TCGA-55-8091          TCGA-55-8094 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8097          TCGA-55-8203          TCGA-55-8204 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8205          TCGA-55-8206          TCGA-55-8207 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8208          TCGA-55-8299          TCGA-55-8301 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8302          TCGA-55-8505          TCGA-55-8506 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8507          TCGA-55-8508          TCGA-55-8510 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8511          TCGA-55-8512          TCGA-55-8513 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8514          TCGA-55-8614          TCGA-55-8615 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8616          TCGA-55-8619          TCGA-55-8620 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-8621          TCGA-55-A48X          TCGA-55-A48Y 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-A48Z          TCGA-55-A490          TCGA-55-A491 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-A492          TCGA-55-A493          TCGA-55-A494 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-55-A4DF          TCGA-55-A4DG          TCGA-62-8394 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-8395          TCGA-62-8397          TCGA-62-8398 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-8399          TCGA-62-A46O          TCGA-62-A46P 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-A46R          TCGA-62-A46S          TCGA-62-A46U 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-A46V          TCGA-62-A46Y          TCGA-62-A470 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-62-A471          TCGA-62-A472          TCGA-64-1676 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-64-1677          TCGA-64-1679          TCGA-64-1681 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-64-5774          TCGA-64-5775          TCGA-64-5778 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-64-5779          TCGA-64-5781          TCGA-64-5815 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-67-3771          TCGA-67-3773          TCGA-67-4679 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-67-6215          TCGA-67-6216          TCGA-67-6217 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-71-6725          TCGA-71-8520          TCGA-73-4658 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4659          TCGA-73-4662          TCGA-73-4666 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4668          TCGA-73-4670          TCGA-73-4675 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-4676          TCGA-73-4677          TCGA-73-7498 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-73-7499          TCGA-75-5122          TCGA-75-5125 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-75-5126          TCGA-75-5146          TCGA-75-5147 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-75-6203          TCGA-75-6205          TCGA-75-6206 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-75-6207          TCGA-75-6211          TCGA-75-6212 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-75-6214          TCGA-75-7025          TCGA-75-7027 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-75-7030          TCGA-75-7031          TCGA-78-7143 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7145          TCGA-78-7146          TCGA-78-7147 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7148          TCGA-78-7149          TCGA-78-7150 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7152          TCGA-78-7153          TCGA-78-7154 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7155          TCGA-78-7156          TCGA-78-7158 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7159          TCGA-78-7160          TCGA-78-7161 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7162          TCGA-78-7163          TCGA-78-7166 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7167          TCGA-78-7220          TCGA-78-7535 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7536          TCGA-78-7537          TCGA-78-7539 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-7540          TCGA-78-7542          TCGA-78-7633 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-8640          TCGA-78-8648          TCGA-78-8655 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-78-8660          TCGA-78-8662          TCGA-80-5607 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-80-5608          TCGA-80-5611          TCGA-83-5908 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-6562          TCGA-86-7701          TCGA-86-7711 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-7713          TCGA-86-7714          TCGA-86-7953 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-7954          TCGA-86-7955          TCGA-86-8054 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8055          TCGA-86-8056          TCGA-86-8073 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8074          TCGA-86-8075          TCGA-86-8076 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8278          TCGA-86-8279          TCGA-86-8280 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8358          TCGA-86-8359          TCGA-86-8585 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8668          TCGA-86-8669          TCGA-86-8671 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-8672          TCGA-86-8673          TCGA-86-8674 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-86-A456          TCGA-86-A4JF          TCGA-86-A4P7 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-91-6828          TCGA-91-6829          TCGA-91-6835 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-91-6840          TCGA-91-A4BD          TCGA-93-7347 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-93-7348          TCGA-93-8067          TCGA-93-A4JN 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-93-A4JO          TCGA-93-A4JP          TCGA-93-A4JQ 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-95-7562          TCGA-95-7944          TCGA-95-7947 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-95-7948          TCGA-95-8039          TCGA-95-A4VK 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-95-A4VN          TCGA-97-7546          TCGA-97-7554 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-7938          TCGA-97-7941          TCGA-97-8176 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-97-A4M2          TCGA-97-A4M7          TCGA-99-7458 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-99-8025          TCGA-99-8028          TCGA-99-8032 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-99-8033          TCGA-J2-A4AD          TCGA-J2-A4AE 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-J2-A4AG          TCGA-L4-A4E5          TCGA-L4-A4E6 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-L9-A443          TCGA-L9-A444          TCGA-MN-A4N1 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MN-A4N4          TCGA-MN-A4N5          TCGA-MP-A4SV 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4SW          TCGA-MP-A4SY          TCGA-MP-A4T2 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4T4          TCGA-MP-A4T6          TCGA-MP-A4T7 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4T8          TCGA-MP-A4T9          TCGA-MP-A4TA 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4TC          TCGA-MP-A4TD          TCGA-MP-A4TE 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4TF          TCGA-MP-A4TH          TCGA-MP-A4TI 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
         TCGA-MP-A4TK          TCGA-MP-A5C7          TCGA-NJ-A4YQ 
"KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" "KIAA0895L WILD-TYPE" 
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0895L MUTATED                                  0     0
  KIAA0895L WILD-TYPE                                1     7
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KIAA0895L MUTATED                           1     3
  KIAA0895L WILD-TYPE                        28   374
D93V14, multiclass
                                  clus
vv                                 KIAA0895L MUTATED KIAA0895L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                   7
  BLACK OR AFRICAN AMERICAN                        1                  28
  WHITE                                            3                 374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V15, binary
                     cls
clus                    0   1
  KIAA0895L MUTATED     0   4
  KIAA0895L WILD-TYPE   6 345
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0895L MUTATED      0    4
  KIAA0895L WILD-TYPE    6  345
                        clus
vv                       KIAA0895L MUTATED KIAA0895L WILD-TYPE
  HISPANIC OR LATINO                     0                   6
  NOT HISPANIC OR LATINO                 4                 345
[1] 2 2
[1] FALSE

Clustering(94) Variable = BMP2K MUTATION ANALYSIS
D94V1, survival
                 sevent
clus2               0   1
  BMP2K MUTATED     9   2
  BMP2K WILD-TYPE 306 139
  BMP2K MUTATED BMP2K WILD-TYPE 
             11             445 
  BMP2K MUTATED BMP2K WILD-TYPE 
              2             139 
$`BMP2K MUTATED`
TCGA-05-4382 TCGA-50-5930 TCGA-55-7911 TCGA-78-8655 TCGA-78-8662 TCGA-86-8668 
       19.96         9.27        17.65        77.59       110.50        13.91 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-7948 TCGA-NJ-A4YQ 
       19.00         1.12        12.39        15.65        29.13 

$`BMP2K WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 
        1.78         1.45        18.64         0.53         6.48         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       39.75        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
        1.15        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 
        1.08        17.29         1.22         2.86        18.67        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  BMP2K MUTATED BMP2K WILD-TYPE 
           1.12            0.00 
  BMP2K MUTATED BMP2K WILD-TYPE 
         110.50          223.96 
  BMP2K MUTATED BMP2K WILD-TYPE 
          17.65           18.08 
[1] "1.1 - 110.5 (17.6)" "0.0 - 224.0 (18.1)"
[1] "hr=" "2.4"
D94V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BMP2K MUTATED         0        5        4         0         1          2
  BMP2K WILD-TYPE       4      118      129        46        66         68
                 vv
clus              STAGE IIIB STAGE IV
  BMP2K MUTATED            0        1
  BMP2K WILD-TYPE         11       24
D94V3, multiclass
            clus
vv           BMP2K MUTATED BMP2K WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BMP2K MUTATED     5   6   1   0
  BMP2K WILD-TYPE 150 255  42  18
D94V4, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  T1             5             150
  T2             6             255
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  BMP2K MUTATED    10   0     2
  BMP2K WILD-TYPE 297  89    70
D94V5, multiclass
       clus
vv      BMP2K MUTATED BMP2K WILD-TYPE
  N0               10             297
  N1                0              89
  N2+N3             2              70
[1] 3 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
  BMP2K MUTATED    10   1
  BMP2K WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED     10    1
  BMP2K WILD-TYPE  317   22
   clus
vv  BMP2K MUTATED BMP2K WILD-TYPE
  0            10             317
  1             1              22
[1] 2 2
[1] FALSE
D94V7, binary
                 cls
clus                0   1
  BMP2K MUTATED     8   5
  BMP2K WILD-TYPE 251 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      8    5
  BMP2K WILD-TYPE  251  216
        clus
vv       BMP2K MUTATED BMP2K WILD-TYPE
  FEMALE             8             251
  MALE               5             216
[1] 2 2
[1] FALSE
D94V8, continuous
[1] "Remove cluster labels:" "BMP2K MUTATED"         
clus
  BMP2K MUTATED BMP2K WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8671 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BMP2K MUTATED                            0                                 5
  BMP2K WILD-TYPE                         18                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BMP2K MUTATED                                                    5
  BMP2K WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BMP2K MUTATED                                            1
  BMP2K WILD-TYPE                                          3
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BMP2K MUTATED                                               0
  BMP2K WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  BMP2K MUTATED                                0
  BMP2K WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  BMP2K MUTATED                                    0
  BMP2K WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BMP2K MUTATED                              0                             1
  BMP2K WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BMP2K MUTATED                                               1
  BMP2K WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  BMP2K MUTATED                              0
  BMP2K WILD-TYPE                            9
D94V9, multiclass
                                                    clus
vv                                                   BMP2K MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   BMP2K WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V10, binary
                 cls
clus                0   1
  BMP2K MUTATED     1  12
  BMP2K WILD-TYPE  19 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      1   12
  BMP2K WILD-TYPE   19  448
     clus
vv    BMP2K MUTATED BMP2K WILD-TYPE
  NO              1              19
  YES            12             448
[1] 2 2
[1] FALSE
D94V11, continuous
D94V12, continuous
                 vv
clus               R0  R1  R2  RX
  BMP2K MUTATED     9   0   0   2
  BMP2K WILD-TYPE 301  11   4  23
D94V13, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMP2K MUTATED                                  0     1
  BMP2K WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BMP2K MUTATED                           0     7
  BMP2K WILD-TYPE                        29   370
D94V14, multiclass
                                  clus
vv                                 BMP2K MUTATED BMP2K WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V15, binary
                 cls
clus                0   1
  BMP2K MUTATED     0   8
  BMP2K WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      0    8
  BMP2K WILD-TYPE    6  341
                        clus
vv                       BMP2K MUTATED BMP2K WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(95) Variable = DOT1L MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2               0   1
  DOT1L MUTATED     9   4
  DOT1L WILD-TYPE 306 137
  DOT1L MUTATED DOT1L WILD-TYPE 
             13             443 
  DOT1L MUTATED DOT1L WILD-TYPE 
              4             137 
$`DOT1L MUTATED`
TCGA-05-4384 TCGA-49-4486 TCGA-49-6767 TCGA-50-5072 TCGA-53-7624 TCGA-55-7727 
       14.01        76.21        22.26         8.22        34.29         1.12 
TCGA-55-8511 TCGA-62-8395 TCGA-64-5781 TCGA-69-7974 TCGA-78-7156 TCGA-86-A4JF 
        0.30        39.98        51.25         6.05        32.09        17.62 
TCGA-91-6836 
       13.71 

$`DOT1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       11.64        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49        17.72         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
        0.92        15.81        20.19        19.99         4.57        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         7.56         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       21.90        39.52        24.99        19.50        38.50         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  DOT1L MUTATED DOT1L WILD-TYPE 
            0.3             0.0 
  DOT1L MUTATED DOT1L WILD-TYPE 
          76.21          223.96 
  DOT1L MUTATED DOT1L WILD-TYPE 
          17.62           18.08 
[1] "0.3 - 76.2 (17.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D95V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DOT1L MUTATED         0        1        4         0         3          4
  DOT1L WILD-TYPE       4      122      129        46        64         66
                 vv
clus              STAGE IIIB STAGE IV
  DOT1L MUTATED            0        2
  DOT1L WILD-TYPE         11       23
D95V3, multiclass
            clus
vv           DOT1L MUTATED DOT1L WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              3              64
  STAGE IIIA             4              66
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOT1L MUTATED     2   8   3   1
  DOT1L WILD-TYPE 153 253  40  17
D95V4, multiclass
    clus
vv   DOT1L MUTATED DOT1L WILD-TYPE
  T1             2             153
  T2             8             253
  T3             3              40
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  DOT1L MUTATED     9   1     4
  DOT1L WILD-TYPE 298  88    68
D95V5, multiclass
       clus
vv      DOT1L MUTATED DOT1L WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             4              68
[1] 3 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
  DOT1L MUTATED     7   2
  DOT1L WILD-TYPE 320  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      7    2
  DOT1L WILD-TYPE  320   21
   clus
vv  DOT1L MUTATED DOT1L WILD-TYPE
  0             7             320
  1             2              21
[1] 2 2
[1] FALSE
D95V7, binary
                 cls
clus                0   1
  DOT1L MUTATED     7   7
  DOT1L WILD-TYPE 252 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      7    7
  DOT1L WILD-TYPE  252  214
        clus
vv       DOT1L MUTATED DOT1L WILD-TYPE
  FEMALE             7             252
  MALE               7             214
[1] 2 2
[1] FALSE
D95V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DOT1L MUTATED                            0                                 6
  DOT1L WILD-TYPE                         18                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DOT1L MUTATED                                                    8
  DOT1L WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DOT1L MUTATED                                            0
  DOT1L WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DOT1L MUTATED                                               0
  DOT1L WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  DOT1L MUTATED                                0
  DOT1L WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  DOT1L MUTATED                                    0
  DOT1L WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DOT1L MUTATED                              0                             0
  DOT1L WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DOT1L MUTATED                                               0
  DOT1L WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  DOT1L MUTATED                              0
  DOT1L WILD-TYPE                            9
D95V9, multiclass
                                                    clus
vv                                                   DOT1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   DOT1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V10, binary
                 cls
clus                0   1
  DOT1L MUTATED     2  12
  DOT1L WILD-TYPE  18 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      2   12
  DOT1L WILD-TYPE   18  448
     clus
vv    DOT1L MUTATED DOT1L WILD-TYPE
  NO              2              18
  YES            12             448
[1] 2 2
[1] FALSE
D95V11, continuous
D95V12, continuous
                 vv
clus               R0  R1  R2  RX
  DOT1L MUTATED     9   0   0   2
  DOT1L WILD-TYPE 301  11   4  23
D95V13, multiclass
    clus
vv   DOT1L MUTATED DOT1L WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOT1L MUTATED                                  0     0
  DOT1L WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOT1L MUTATED                           0    12
  DOT1L WILD-TYPE                        29   365
D95V14, multiclass
                                  clus
vv                                 DOT1L MUTATED DOT1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V15, binary
                 cls
clus                0   1
  DOT1L MUTATED     1   9
  DOT1L WILD-TYPE   5 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      1    9
  DOT1L WILD-TYPE    5  340
                        clus
vv                       DOT1L MUTATED DOT1L WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(96) Variable = SND1 MUTATION ANALYSIS
D96V1, survival
                sevent
clus2              0   1
  SND1 MUTATED    10   6
  SND1 WILD-TYPE 305 135
  SND1 MUTATED SND1 WILD-TYPE 
            16            440 
  SND1 MUTATED SND1 WILD-TYPE 
             6            135 
$`SND1 MUTATED`
TCGA-05-4415 TCGA-44-3918 TCGA-50-5930 TCGA-50-6594 TCGA-64-1676 TCGA-69-7978 
        2.99        34.06         9.27        12.16        56.81         2.30 
TCGA-78-7155 TCGA-78-7166 TCGA-86-7701 TCGA-86-7955 TCGA-86-8358 TCGA-86-8359 
       38.50         8.48        31.13        16.70        21.47        14.60 
TCGA-91-6828 TCGA-95-7043 TCGA-95-7947 TCGA-NJ-A4YQ 
       10.62         1.22        15.68        29.13 

$`SND1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         8.22        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
       72.30        13.61        39.25        40.96        29.92        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        7.07       104.19       223.96        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 
       15.75        16.08        15.65        15.85        23.05         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       13.32        17.62        13.64        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SND1 MUTATED SND1 WILD-TYPE 
          1.22           0.00 
  SND1 MUTATED SND1 WILD-TYPE 
         56.81         223.96 
  SND1 MUTATED SND1 WILD-TYPE 
         15.14          18.15 
[1] "1.2 - 56.8 (15.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D96V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SND1 MUTATED         0        6        3         0         2          3
  SND1 WILD-TYPE       4      117      130        46        65         67
                vv
clus             STAGE IIIB STAGE IV
  SND1 MUTATED            1        1
  SND1 WILD-TYPE         10       24
D96V3, multiclass
            clus
vv           SND1 MUTATED SND1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             2             65
  STAGE IIIA            3             67
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SND1 MUTATED     6   7   2   1
  SND1 WILD-TYPE 149 254  41  17
D96V4, multiclass
    clus
vv   SND1 MUTATED SND1 WILD-TYPE
  T1            6            149
  T2            7            254
  T3            2             41
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  SND1 MUTATED    10   2     4
  SND1 WILD-TYPE 297  87    68
D96V5, multiclass
       clus
vv      SND1 MUTATED SND1 WILD-TYPE
  N0              10            297
  N1               2             87
  N2+N3            4             68
[1] 3 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
  SND1 MUTATED    13   1
  SND1 WILD-TYPE 314  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED     13    1
  SND1 WILD-TYPE  314   22
   clus
vv  SND1 MUTATED SND1 WILD-TYPE
  0           13            314
  1            1             22
[1] 2 2
[1] FALSE
D96V7, binary
                cls
clus               0   1
  SND1 MUTATED     4  12
  SND1 WILD-TYPE 255 209
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      4   12
  SND1 WILD-TYPE  255  209
        clus
vv       SND1 MUTATED SND1 WILD-TYPE
  FEMALE            4            255
  MALE             12            209
[1] 2 2
[1] FALSE
D96V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SND1 MUTATED                            0                                 5
  SND1 WILD-TYPE                         18                                97
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SND1 MUTATED                                                   11
  SND1 WILD-TYPE                                                283
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SND1 MUTATED                                            0
  SND1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SND1 MUTATED                                               0
  SND1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SND1 MUTATED                                0
  SND1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SND1 MUTATED                                    0
  SND1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SND1 MUTATED                              0                             0
  SND1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SND1 MUTATED                                               0
  SND1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SND1 MUTATED                              0
  SND1 WILD-TYPE                            9
D96V9, multiclass
                                                    clus
vv                                                   SND1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SND1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V10, binary
                cls
clus               0   1
  SND1 MUTATED     2  14
  SND1 WILD-TYPE  18 446
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      2   14
  SND1 WILD-TYPE   18  446
     clus
vv    SND1 MUTATED SND1 WILD-TYPE
  NO             2             18
  YES           14            446
[1] 2 2
[1] FALSE
D96V11, continuous
D96V12, continuous
                vv
clus              R0  R1  R2  RX
  SND1 MUTATED    10   0   0   2
  SND1 WILD-TYPE 300  11   4  23
D96V13, multiclass
    clus
vv   SND1 MUTATED SND1 WILD-TYPE
  R0           10            300
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SND1 MUTATED                                  0     0
  SND1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SND1 MUTATED                           1    14
  SND1 WILD-TYPE                        28   363
D96V14, multiclass
                                  clus
vv                                 SND1 MUTATED SND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      14            363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V15, binary
                cls
clus               0   1
  SND1 MUTATED     0  13
  SND1 WILD-TYPE   6 336
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      0   13
  SND1 WILD-TYPE    6  336
                        clus
vv                       SND1 MUTATED SND1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           13            336
[1] 2 2
[1] FALSE

Clustering(97) Variable = VGLL3 MUTATION ANALYSIS
D97V1, survival
                 sevent
clus2               0   1
  VGLL3 MUTATED    12   3
  VGLL3 WILD-TYPE 303 138
  VGLL3 MUTATED VGLL3 WILD-TYPE 
             15             441 
  VGLL3 MUTATED VGLL3 WILD-TYPE 
              3             138 
$`VGLL3 MUTATED`
TCGA-05-4432 TCGA-44-4112 TCGA-55-7910 TCGA-55-A48X TCGA-62-A46O TCGA-69-7979 
       25.02        26.56         6.48        22.65        47.80         2.93 
TCGA-69-7980 TCGA-86-8279 TCGA-95-7039 TCGA-97-A4M3 TCGA-L9-A443 TCGA-L9-A444 
       12.56        15.85         1.12        17.75         3.81         0.20 
TCGA-MP-A4T7 TCGA-NJ-A4YQ TCGA-NJ-A55R 
        5.49        29.13        19.82 

$`VGLL3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 
       42.77        37.15        38.24        34.06         6.25        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
        1.78         1.45        18.64         0.53        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56         6.05         2.30        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        86.04        58.85         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.26         0.43        59.11 

  VGLL3 MUTATED VGLL3 WILD-TYPE 
            0.2             0.0 
  VGLL3 MUTATED VGLL3 WILD-TYPE 
          47.80          223.96 
  VGLL3 MUTATED VGLL3 WILD-TYPE 
          15.85           18.12 
[1] "0.2 - 47.8 (15.8)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D97V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  VGLL3 MUTATED         1        5        3         3         2          2
  VGLL3 WILD-TYPE       3      118      130        43        65         68
                 vv
clus              STAGE IIIB STAGE IV
  VGLL3 MUTATED            0        1
  VGLL3 WILD-TYPE         11       24
D97V3, multiclass
            clus
vv           VGLL3 MUTATED VGLL3 WILD-TYPE
  STAGE I                1               3
  STAGE IA               5             118
  STAGE IB               3             130
  STAGE IIA              3              43
  STAGE IIB              2              65
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VGLL3 MUTATED     7   8   2   0
  VGLL3 WILD-TYPE 148 253  41  18
D97V4, multiclass
    clus
vv   VGLL3 MUTATED VGLL3 WILD-TYPE
  T1             7             148
  T2             8             253
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  VGLL3 MUTATED    12   3     2
  VGLL3 WILD-TYPE 295  86    70
D97V5, multiclass
       clus
vv      VGLL3 MUTATED VGLL3 WILD-TYPE
  N0               12             295
  N1                3              86
  N2+N3             2              70
[1] 3 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
  VGLL3 MUTATED    11   1
  VGLL3 WILD-TYPE 316  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL3 MUTATED     11    1
  VGLL3 WILD-TYPE  316   22
   clus
vv  VGLL3 MUTATED VGLL3 WILD-TYPE
  0            11             316
  1             1              22
[1] 2 2
[1] FALSE
D97V7, binary
                 cls
clus                0   1
  VGLL3 MUTATED    14   3
  VGLL3 WILD-TYPE 245 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL3 MUTATED     14    3
  VGLL3 WILD-TYPE  245  218
        clus
vv       VGLL3 MUTATED VGLL3 WILD-TYPE
  FEMALE            14             245
  MALE               3             218
[1] 2 2
[1] FALSE
D97V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  VGLL3 MUTATED                            1                                 3
  VGLL3 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  VGLL3 MUTATED                                                   12
  VGLL3 WILD-TYPE                                                282
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  VGLL3 MUTATED                                            0
  VGLL3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  VGLL3 MUTATED                                               0
  VGLL3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  VGLL3 MUTATED                                0
  VGLL3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  VGLL3 MUTATED                                    0
  VGLL3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  VGLL3 MUTATED                              0                             1
  VGLL3 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  VGLL3 MUTATED                                               0
  VGLL3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  VGLL3 MUTATED                              0
  VGLL3 WILD-TYPE                            9
D97V9, multiclass
                                                    clus
vv                                                   VGLL3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   VGLL3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V10, binary
                 cls
clus                0   1
  VGLL3 MUTATED     0  17
  VGLL3 WILD-TYPE  20 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL3 MUTATED      0   17
  VGLL3 WILD-TYPE   20  443
     clus
vv    VGLL3 MUTATED VGLL3 WILD-TYPE
  NO              0              20
  YES            17             443
[1] 2 2
[1] FALSE
D97V11, continuous
D97V12, continuous
                 vv
clus               R0  R1  R2  RX
  VGLL3 MUTATED    10   0   1   1
  VGLL3 WILD-TYPE 300  11   3  24
D97V13, multiclass
    clus
vv   VGLL3 MUTATED VGLL3 WILD-TYPE
  R0            10             300
  R1             0              11
  R2             1               3
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VGLL3 MUTATED                                  0     0
  VGLL3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VGLL3 MUTATED                           1    12
  VGLL3 WILD-TYPE                        28   365
D97V14, multiclass
                                  clus
vv                                 VGLL3 MUTATED VGLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V15, binary
                 cls
clus                0   1
  VGLL3 MUTATED     0  13
  VGLL3 WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL3 MUTATED      0   13
  VGLL3 WILD-TYPE    6  336
                        clus
vv                       VGLL3 MUTATED VGLL3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(98) Variable = LUM MUTATION ANALYSIS
D98V1, survival
               sevent
clus2             0   1
  LUM MUTATED    11   4
  LUM WILD-TYPE 304 137
  LUM MUTATED LUM WILD-TYPE 
           15           441 
  LUM MUTATED LUM WILD-TYPE 
            4           137 
$`LUM MUTATED`
TCGA-05-4390 TCGA-05-5425 TCGA-44-7660 TCGA-44-8117 TCGA-44-A479 TCGA-50-5930 
       37.02        29.00        19.46        12.66        15.98         9.27 
TCGA-50-5933 TCGA-55-8510 TCGA-67-6217 TCGA-73-4668 TCGA-78-7152 TCGA-86-8054 
       78.67        17.72        13.87        15.35        39.52        24.49 
TCGA-97-7554 TCGA-97-7938 TCGA-J2-A4AD 
       25.48         0.59        18.08 

$`LUM WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        14.60        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A 
       29.00        17.59        23.64         3.25         8.55        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        8.22        14.27        40.60        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.49         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       18.84        14.04         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       43.79         5.95         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        23.80        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  LUM MUTATED LUM WILD-TYPE 
         0.59          0.00 
  LUM MUTATED LUM WILD-TYPE 
        78.67        223.96 
  LUM MUTATED LUM WILD-TYPE 
        18.08         17.98 
[1] "0.6 - 78.7 (18.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D98V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LUM MUTATED         0        2        6         1         3          2
  LUM WILD-TYPE       4      121      127        45        64         68
               vv
clus            STAGE IIIB STAGE IV
  LUM MUTATED            1        0
  LUM WILD-TYPE         10       25
D98V3, multiclass
            clus
vv           LUM MUTATED LUM WILD-TYPE
  STAGE I              0             4
  STAGE IA             2           121
  STAGE IB             6           127
  STAGE IIA            1            45
  STAGE IIB            3            64
  STAGE IIIA           2            68
  STAGE IIIB           1            10
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  LUM MUTATED     2  12   0   1
  LUM WILD-TYPE 153 249  43  17
D98V4, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  T1           2           153
  T2          12           249
  T3           0            43
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  LUM MUTATED     8   4     3
  LUM WILD-TYPE 299  85    69
D98V5, multiclass
       clus
vv      LUM MUTATED LUM WILD-TYPE
  N0              8           299
  N1              4            85
  N2+N3           3            69
[1] 3 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
  LUM MUTATED    10   0
  LUM WILD-TYPE 317  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED     10    0
  LUM WILD-TYPE  317   23
   clus
vv  LUM MUTATED LUM WILD-TYPE
  0          10           317
  1           0            23
[1] 2 2
[1] FALSE
D98V7, binary
               cls
clus              0   1
  LUM MUTATED     9   6
  LUM WILD-TYPE 250 215
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      9    6
  LUM WILD-TYPE  250  215
        clus
vv       LUM MUTATED LUM WILD-TYPE
  FEMALE           9           250
  MALE             6           215
[1] 2 2
[1] FALSE
D98V8, continuous
[1] "Remove cluster labels:" "LUM MUTATED"           
clus
  LUM MUTATED LUM WILD-TYPE 
            1            83 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-62-A470    TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-64-5778    TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-73-4659    TCGA-73-4662    TCGA-73-4666    TCGA-73-4676    TCGA-73-7498 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-86-8279    TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-86-8669    TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
   TCGA-MN-A4N1    TCGA-MN-A4N4    TCGA-MN-A4N5 
"LUM WILD-TYPE" "LUM WILD-TYPE" "LUM WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LUM MUTATED                            1                                 4
  LUM WILD-TYPE                         17                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LUM MUTATED                                                    7
  LUM WILD-TYPE                                                287
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LUM MUTATED                                            0
  LUM WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LUM MUTATED                                               1
  LUM WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  LUM MUTATED                                0
  LUM WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  LUM MUTATED                                    1                            0
  LUM WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  LUM MUTATED                               1
  LUM WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LUM MUTATED                                               0
  LUM WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  LUM MUTATED                              0
  LUM WILD-TYPE                            9
D98V9, multiclass
                                                    clus
vv                                                   LUM MUTATED LUM WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           7           287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           1             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V10, binary
               cls
clus              0   1
  LUM MUTATED     2  13
  LUM WILD-TYPE  18 447
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      2   13
  LUM WILD-TYPE   18  447
     clus
vv    LUM MUTATED LUM WILD-TYPE
  NO            2            18
  YES          13           447
[1] 2 2
[1] FALSE
D98V11, continuous
D98V12, continuous
               vv
clus             R0  R1  R2  RX
  LUM MUTATED    10   0   0   1
  LUM WILD-TYPE 300  11   4  24
D98V13, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  R0          10           300
  R1           0            11
  R2           0             4
  RX           1            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LUM MUTATED                                  1     0
  LUM WILD-TYPE                                0     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LUM MUTATED                           1    11
  LUM WILD-TYPE                        28   366
D98V14, multiclass
                                  clus
vv                                 LUM MUTATED LUM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     11           366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V15, binary
               cls
clus              0   1
  LUM MUTATED     0  12
  LUM WILD-TYPE   6 337
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      0   12
  LUM WILD-TYPE    6  337
                        clus
vv                       LUM MUTATED LUM WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          12           337
[1] 2 2
[1] FALSE

Clustering(99) Variable = ATP1B4 MUTATION ANALYSIS
D99V1, survival
                  sevent
clus2                0   1
  ATP1B4 MUTATED     6   3
  ATP1B4 WILD-TYPE 309 138
  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
               9              447 
  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
               3              138 
$`ATP1B4 MUTATED`
TCGA-44-2656 TCGA-49-6744 TCGA-50-6590 TCGA-55-1592 TCGA-55-7574 TCGA-55-8208 
       46.98        29.26        42.35        23.05         3.12        22.16 
TCGA-67-6217 TCGA-78-7535 TCGA-86-8054 
       13.87        31.20        24.49 

$`ATP1B4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       29.46        29.75        55.89        14.63        12.13        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        22.55         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.43        19.89        16.70         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
            3.12             0.00 
  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
           46.98           223.96 
  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
           24.49            17.75 
[1] "3.1 - 47.0 (24.5)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1"  
D99V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ATP1B4 MUTATED         0        2        4         2         1          0
  ATP1B4 WILD-TYPE       4      121      129        44        66         70
                  vv
clus               STAGE IIIB STAGE IV
  ATP1B4 MUTATED            0        0
  ATP1B4 WILD-TYPE         11       25
D99V3, multiclass
            clus
vv           ATP1B4 MUTATED ATP1B4 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                4              129
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP1B4 MUTATED     1   8   0   0
  ATP1B4 WILD-TYPE 154 253  43  18
D99V4, multiclass
    clus
vv   ATP1B4 MUTATED ATP1B4 WILD-TYPE
  T1              1              154
  T2              8              253
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ATP1B4 MUTATED     6   3     0
  ATP1B4 WILD-TYPE 301  86    72
D99V5, multiclass
       clus
vv      ATP1B4 MUTATED ATP1B4 WILD-TYPE
  N0                 6              301
  N1                 3               86
  N2+N3              0               72
[1] 3 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
  ATP1B4 MUTATED     8   0
  ATP1B4 WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1B4 MUTATED      8    0
  ATP1B4 WILD-TYPE  319   23
   clus
vv  ATP1B4 MUTATED ATP1B4 WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D99V7, binary
                  cls
clus                 0   1
  ATP1B4 MUTATED     5   4
  ATP1B4 WILD-TYPE 254 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1B4 MUTATED      5    4
  ATP1B4 WILD-TYPE  254  217
        clus
vv       ATP1B4 MUTATED ATP1B4 WILD-TYPE
  FEMALE              5              254
  MALE                4              217
[1] 2 2
[1] FALSE
D99V8, continuous
[1] "Remove cluster labels:" "ATP1B4 MUTATED"        
clus
  ATP1B4 MUTATED ATP1B4 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" "ATP1B4 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ATP1B4 MUTATED                            1                                 1
  ATP1B4 WILD-TYPE                         17                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ATP1B4 MUTATED                                                    7
  ATP1B4 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ATP1B4 MUTATED                                            0
  ATP1B4 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ATP1B4 MUTATED                                               0
  ATP1B4 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ATP1B4 MUTATED                                0
  ATP1B4 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ATP1B4 MUTATED                                    0
  ATP1B4 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ATP1B4 MUTATED                              0                             0
  ATP1B4 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ATP1B4 MUTATED                                               0
  ATP1B4 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ATP1B4 MUTATED                              0
  ATP1B4 WILD-TYPE                            9
D99V9, multiclass
                                                    clus
vv                                                   ATP1B4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ATP1B4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V10, binary
                  cls
clus                 0   1
  ATP1B4 MUTATED     1   8
  ATP1B4 WILD-TYPE  19 452
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1B4 MUTATED      1    8
  ATP1B4 WILD-TYPE   19  452
     clus
vv    ATP1B4 MUTATED ATP1B4 WILD-TYPE
  NO               1               19
  YES              8              452
[1] 2 2
[1] FALSE
D99V11, continuous
D99V12, continuous
                  vv
clus                R0  R1  R2  RX
  ATP1B4 MUTATED     6   1   0   0
  ATP1B4 WILD-TYPE 304  10   4  25
D99V13, multiclass
    clus
vv   ATP1B4 MUTATED ATP1B4 WILD-TYPE
  R0              6              304
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP1B4 MUTATED                                  0     0
  ATP1B4 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP1B4 MUTATED                           0     9
  ATP1B4 WILD-TYPE                        29   368
D99V14, multiclass
                                  clus
vv                                 ATP1B4 MUTATED ATP1B4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V15, binary
                  cls
clus                 0   1
  ATP1B4 MUTATED     0   7
  ATP1B4 WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1B4 MUTATED      0    7
  ATP1B4 WILD-TYPE    6  342
                        clus
vv                       ATP1B4 MUTATED ATP1B4 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(100) Variable = ATAD2 MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2               0   1
  ATAD2 MUTATED    11   2
  ATAD2 WILD-TYPE 304 139
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             13             443 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
              2             139 
$`ATAD2 MUTATED`
TCGA-05-4397 TCGA-44-5644 TCGA-44-6144 TCGA-55-7994 TCGA-64-1679 TCGA-64-5775 
       24.03        28.37        23.77        19.82        55.43         2.04 
TCGA-69-7979 TCGA-69-7980 TCGA-78-7633 TCGA-95-7567 TCGA-97-7937 TCGA-99-8025 
        2.93        12.56        32.68        18.67         5.95        34.85 
TCGA-MN-A4N4 
       38.63 

$`ATAD2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       33.30        12.59        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       20.65        38.37        87.98        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        7.56         6.05         2.30        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        10.75        39.35        10.55       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         1.22         2.86        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79        25.48         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ATAD2 MUTATED ATAD2 WILD-TYPE 
           2.04            0.00 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
          55.43          223.96 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
          23.77           17.75 
[1] "2.0 - 55.4 (23.8)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "2"  
D100V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ATAD2 MUTATED         1        4        3         0         3          3
  ATAD2 WILD-TYPE       3      119      130        46        64         67
                 vv
clus              STAGE IIIB STAGE IV
  ATAD2 MUTATED            0        0
  ATAD2 WILD-TYPE         11       25
D100V3, multiclass
            clus
vv           ATAD2 MUTATED ATAD2 WILD-TYPE
  STAGE I                1               3
  STAGE IA               4             119
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATAD2 MUTATED     5   6   2   1
  ATAD2 WILD-TYPE 150 255  41  17
D100V4, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  T1             5             150
  T2             6             255
  T3             2              41
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  ATAD2 MUTATED     9   2     2
  ATAD2 WILD-TYPE 298  87    70
D100V5, multiclass
       clus
vv      ATAD2 MUTATED ATAD2 WILD-TYPE
  N0                9             298
  N1                2              87
  N2+N3             2              70
[1] 3 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
  ATAD2 MUTATED    10   0
  ATAD2 WILD-TYPE 317  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED     10    0
  ATAD2 WILD-TYPE  317   23
   clus
vv  ATAD2 MUTATED ATAD2 WILD-TYPE
  0            10             317
  1             0              23
[1] 2 2
[1] FALSE
D100V7, binary
                 cls
clus                0   1
  ATAD2 MUTATED     5   9
  ATAD2 WILD-TYPE 254 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      5    9
  ATAD2 WILD-TYPE  254  212
        clus
vv       ATAD2 MUTATED ATAD2 WILD-TYPE
  FEMALE             5             254
  MALE               9             212
[1] 2 2
[1] FALSE
D100V8, continuous
[1] "Remove cluster labels:" "ATAD2 MUTATED"         
clus
  ATAD2 MUTATED ATAD2 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8358 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N5 
"ATAD2 WILD-TYPE" "ATAD2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ATAD2 MUTATED                            1                                 3
  ATAD2 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ATAD2 MUTATED                                                    9
  ATAD2 WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ATAD2 MUTATED                                            0
  ATAD2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ATAD2 MUTATED                                               0
  ATAD2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ATAD2 MUTATED                                0
  ATAD2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ATAD2 MUTATED                                    1
  ATAD2 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ATAD2 MUTATED                              0                             0
  ATAD2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ATAD2 MUTATED                                               0
  ATAD2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ATAD2 MUTATED                              0
  ATAD2 WILD-TYPE                            9
D100V9, multiclass
                                                    clus
vv                                                   ATAD2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ATAD2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V10, binary
                 cls
clus                0   1
  ATAD2 MUTATED     0  14
  ATAD2 WILD-TYPE  20 446
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      0   14
  ATAD2 WILD-TYPE   20  446
     clus
vv    ATAD2 MUTATED ATAD2 WILD-TYPE
  NO              0              20
  YES            14             446
[1] 2 2
[1] FALSE
D100V11, continuous
D100V12, continuous
                 vv
clus               R0  R1  R2  RX
  ATAD2 MUTATED     7   0   0   1
  ATAD2 WILD-TYPE 303  11   4  24
D100V13, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD2 MUTATED                                  0     0
  ATAD2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATAD2 MUTATED                           1    12
  ATAD2 WILD-TYPE                        28   365
D100V14, multiclass
                                  clus
vv                                 ATAD2 MUTATED ATAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V15, binary
                 cls
clus                0   1
  ATAD2 MUTATED     0  12
  ATAD2 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      0   12
  ATAD2 WILD-TYPE    6  337
                        clus
vv                       ATAD2 MUTATED ATAD2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(101) Variable = SLC17A9 MUTATION ANALYSIS
D101V1, survival
                   sevent
clus2                 0   1
  SLC17A9 MUTATED     8   0
  SLC17A9 WILD-TYPE 307 141
  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
                8               448 
  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
                0               141 
$`SLC17A9 MUTATED`
TCGA-05-5715 TCGA-44-2656 TCGA-44-6776 TCGA-55-5899 TCGA-55-7907 TCGA-55-7994 
        2.04        46.98        63.72         2.86         0.53        19.82 
TCGA-55-A48X TCGA-MN-A4N1 
       22.65        27.19 

$`SLC17A9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
       18.64         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       16.93        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 
       16.44        19.00        14.30         3.81         0.20        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
             0.53              0.00 
  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
            63.72            223.96 
  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
           21.235            17.950 
[1] "0.5 - 63.7 (21.2)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "9200000"
D101V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC17A9 MUTATED         0        2        2         3         1          0
  SLC17A9 WILD-TYPE       4      121      131        43        66         70
                   vv
clus                STAGE IIIB STAGE IV
  SLC17A9 MUTATED            0        0
  SLC17A9 WILD-TYPE         11       25
D101V3, multiclass
            clus
vv           SLC17A9 MUTATED SLC17A9 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 2               131
  STAGE IIA                3                43
  STAGE IIB                1                66
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC17A9 MUTATED     3   4   1   0
  SLC17A9 WILD-TYPE 152 257  42  18
D101V4, multiclass
    clus
vv   SLC17A9 MUTATED SLC17A9 WILD-TYPE
  T1               3               152
  T2               4               257
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  SLC17A9 MUTATED     4   4     0
  SLC17A9 WILD-TYPE 303  85    72
D101V5, multiclass
       clus
vv      SLC17A9 MUTATED SLC17A9 WILD-TYPE
  N0                  4               303
  N1                  4                85
  N2+N3               0                72
[1] 3 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
  SLC17A9 MUTATED     5   0
  SLC17A9 WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A9 MUTATED      5    0
  SLC17A9 WILD-TYPE  322   23
   clus
vv  SLC17A9 MUTATED SLC17A9 WILD-TYPE
  0               5               322
  1               0                23
[1] 2 2
[1] FALSE
D101V7, binary
                   cls
clus                  0   1
  SLC17A9 MUTATED     3   5
  SLC17A9 WILD-TYPE 256 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A9 MUTATED      3    5
  SLC17A9 WILD-TYPE  256  216
        clus
vv       SLC17A9 MUTATED SLC17A9 WILD-TYPE
  FEMALE               3               256
  MALE                 5               216
[1] 2 2
[1] FALSE
D101V8, continuous
[1] "Remove cluster labels:" "SLC17A9 MUTATED"       
clus
  SLC17A9 MUTATED SLC17A9 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-93-7348        TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
       TCGA-99-7458        TCGA-MN-A4N4        TCGA-MN-A4N5 
"SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" "SLC17A9 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC17A9 MUTATED                            0
  SLC17A9 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC17A9 MUTATED                                   1
  SLC17A9 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC17A9 MUTATED                                                    7
  SLC17A9 WILD-TYPE                                                287
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC17A9 MUTATED                                            0
  SLC17A9 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC17A9 MUTATED                                               0
  SLC17A9 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC17A9 MUTATED                                0
  SLC17A9 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC17A9 MUTATED                                    0
  SLC17A9 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC17A9 MUTATED                              0                             0
  SLC17A9 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC17A9 MUTATED                                               0
  SLC17A9 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC17A9 MUTATED                              0
  SLC17A9 WILD-TYPE                            9
D101V9, multiclass
                                                    clus
vv                                                   SLC17A9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SLC17A9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V10, binary
                   cls
clus                  0   1
  SLC17A9 MUTATED     0   8
  SLC17A9 WILD-TYPE  20 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A9 MUTATED      0    8
  SLC17A9 WILD-TYPE   20  452
     clus
vv    SLC17A9 MUTATED SLC17A9 WILD-TYPE
  NO                0                20
  YES               8               452
[1] 2 2
[1] FALSE
D101V11, continuous
D101V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC17A9 MUTATED     6   0   0   0
  SLC17A9 WILD-TYPE 304  11   4  25
D101V13, multiclass
    clus
vv   SLC17A9 MUTATED SLC17A9 WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC17A9 MUTATED                                  0     0
  SLC17A9 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC17A9 MUTATED                           1     6
  SLC17A9 WILD-TYPE                        28   371
D101V14, multiclass
                                  clus
vv                                 SLC17A9 MUTATED SLC17A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V15, binary
                   cls
clus                  0   1
  SLC17A9 MUTATED     0   6
  SLC17A9 WILD-TYPE   6 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A9 MUTATED      0    6
  SLC17A9 WILD-TYPE    6  343
                        clus
vv                       SLC17A9 MUTATED SLC17A9 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               6               343
[1] 2 2
[1] FALSE

Clustering(102) Variable = ZNF592 MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  ZNF592 MUTATED    13   3
  ZNF592 WILD-TYPE 302 138
  ZNF592 MUTATED ZNF592 WILD-TYPE 
              16              440 
  ZNF592 MUTATED ZNF592 WILD-TYPE 
               3              138 
$`ZNF592 MUTATED`
TCGA-05-4420 TCGA-05-4427 TCGA-44-2656 TCGA-50-5931 TCGA-64-1679 TCGA-69-7979 
       29.98        26.01        46.98        14.27        55.43         2.93 
TCGA-78-7156 TCGA-78-8662 TCGA-86-7713 TCGA-86-8073 TCGA-86-8358 TCGA-86-A4JF 
       32.09       110.50        13.87        24.33        21.47        17.62 
TCGA-91-6830 TCGA-91-8499 TCGA-97-8547 TCGA-99-7458 
        1.97         1.18        21.60        24.56 

$`ZNF592 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22         9.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.30        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        38.50         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       32.68       214.62        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        34.39        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.18        16.60        14.27         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX 
       18.12        15.39        16.41        14.30        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ZNF592 MUTATED ZNF592 WILD-TYPE 
            1.18             0.00 
  ZNF592 MUTATED ZNF592 WILD-TYPE 
          110.50           223.96 
  ZNF592 MUTATED ZNF592 WILD-TYPE 
          22.965           17.835 
[1] "1.2 - 110.5 (23.0)" "0.0 - 224.0 (17.8)"
[1] "hr=" "2.1"
D102V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF592 MUTATED         0        1        7         2         2          3
  ZNF592 WILD-TYPE       4      122      126        44        65         67
                  vv
clus               STAGE IIIB STAGE IV
  ZNF592 MUTATED            0        1
  ZNF592 WILD-TYPE         11       24
D102V3, multiclass
            clus
vv           ZNF592 MUTATED ZNF592 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                7              126
  STAGE IIA               2               44
  STAGE IIB               2               65
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF592 MUTATED     3  10   1   2
  ZNF592 WILD-TYPE 152 251  42  16
D102V4, multiclass
    clus
vv   ZNF592 MUTATED ZNF592 WILD-TYPE
  T1              3              152
  T2             10              251
  T3              1               42
  T4              2               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"
                  vv
clus                N0  N1 N2+N3
  ZNF592 MUTATED    11   3     2
  ZNF592 WILD-TYPE 296  86    70
D102V5, multiclass
       clus
vv      ZNF592 MUTATED ZNF592 WILD-TYPE
  N0                11              296
  N1                 3               86
  N2+N3              2               70
[1] 3 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
  ZNF592 MUTATED    11   1
  ZNF592 WILD-TYPE 316  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF592 MUTATED     11    1
  ZNF592 WILD-TYPE  316   22
   clus
vv  ZNF592 MUTATED ZNF592 WILD-TYPE
  0             11              316
  1              1               22
[1] 2 2
[1] FALSE
D102V7, binary
                  cls
clus                 0   1
  ZNF592 MUTATED     9   7
  ZNF592 WILD-TYPE 250 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF592 MUTATED      9    7
  ZNF592 WILD-TYPE  250  214
        clus
vv       ZNF592 MUTATED ZNF592 WILD-TYPE
  FEMALE              9              250
  MALE                7              214
[1] 2 2
[1] FALSE
D102V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF592 MUTATED                            1                                 4
  ZNF592 WILD-TYPE                         17                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF592 MUTATED                                                    9
  ZNF592 WILD-TYPE                                                285
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF592 MUTATED                                            0
  ZNF592 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF592 MUTATED                                               2
  ZNF592 WILD-TYPE                                            17
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF592 MUTATED                                0
  ZNF592 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF592 MUTATED                                    0
  ZNF592 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF592 MUTATED                              0                             0
  ZNF592 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF592 MUTATED                                               0
  ZNF592 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF592 MUTATED                              0
  ZNF592 WILD-TYPE                            9
D102V9, multiclass
                                                    clus
vv                                                   ZNF592 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF592 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    17
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V10, binary
                  cls
clus                 0   1
  ZNF592 MUTATED     0  16
  ZNF592 WILD-TYPE  20 444
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF592 MUTATED      0   16
  ZNF592 WILD-TYPE   20  444
     clus
vv    ZNF592 MUTATED ZNF592 WILD-TYPE
  NO               0               20
  YES             16              444
[1] 2 2
[1] FALSE
D102V11, continuous
D102V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF592 MUTATED    11   0   0   0
  ZNF592 WILD-TYPE 299  11   4  25
D102V13, multiclass
    clus
vv   ZNF592 MUTATED ZNF592 WILD-TYPE
  R0             11              299
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF592 MUTATED                                  0     0
  ZNF592 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF592 MUTATED                           0    12
  ZNF592 WILD-TYPE                        29   365
D102V14, multiclass
                                  clus
vv                                 ZNF592 MUTATED ZNF592 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        12              365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V15, binary
                  cls
clus                 0   1
  ZNF592 MUTATED     0  11
  ZNF592 WILD-TYPE   6 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF592 MUTATED      0   11
  ZNF592 WILD-TYPE    6  338
                        clus
vv                       ZNF592 MUTATED ZNF592 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(103) Variable = ZNF556 MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2                0   1
  ZNF556 MUTATED     8   4
  ZNF556 WILD-TYPE 307 137
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              444 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               4              137 
$`ZNF556 MUTATED`
TCGA-05-4405 TCGA-05-4424 TCGA-38-4630 TCGA-50-5946 TCGA-55-6982 TCGA-55-7994 
       20.05        30.02        35.28        22.55        32.71        19.82 
TCGA-55-8301 TCGA-69-7979 TCGA-91-6829 TCGA-97-8179 TCGA-99-8028 TCGA-MP-A4TF 
        1.45         2.93        41.36        14.30        36.76        11.05 

$`ZNF556 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH 
       41.59        31.23         2.43        10.09        29.46        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ZNF556 MUTATED ZNF556 WILD-TYPE 
            1.45             0.00 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
           41.36           223.96 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
          21.300           17.835 
[1] "1.4 - 41.4 (21.3)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.2"
D103V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF556 MUTATED         0        3        5         1         3          0
  ZNF556 WILD-TYPE       4      120      128        45        64         70
                  vv
clus               STAGE IIIB STAGE IV
  ZNF556 MUTATED            0        0
  ZNF556 WILD-TYPE         11       25
D103V3, multiclass
            clus
vv           ZNF556 MUTATED ZNF556 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                5              128
  STAGE IIA               1               45
  STAGE IIB               3               64
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF556 MUTATED     3   7   2   0
  ZNF556 WILD-TYPE 152 254  41  18
D103V4, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  T1              3              152
  T2              7              254
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ZNF556 MUTATED    11   1     0
  ZNF556 WILD-TYPE 296  88    72
D103V5, multiclass
       clus
vv      ZNF556 MUTATED ZNF556 WILD-TYPE
  N0                11              296
  N1                 1               88
  N2+N3              0               72
[1] 3 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
  ZNF556 MUTATED     7   0
  ZNF556 WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      7    0
  ZNF556 WILD-TYPE  320   23
   clus
vv  ZNF556 MUTATED ZNF556 WILD-TYPE
  0              7              320
  1              0               23
[1] 2 2
[1] FALSE
D103V7, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     6   6
  ZNF556 WILD-TYPE 253 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      6    6
  ZNF556 WILD-TYPE  253  215
        clus
vv       ZNF556 MUTATED ZNF556 WILD-TYPE
  FEMALE              6              253
  MALE                6              215
[1] 2 2
[1] FALSE
D103V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF556 MUTATED                            2                                 3
  ZNF556 WILD-TYPE                         16                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF556 MUTATED                                                    5
  ZNF556 WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF556 MUTATED                                            0
  ZNF556 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF556 MUTATED                                               1
  ZNF556 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF556 MUTATED                                0
  ZNF556 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF556 MUTATED                                    0
  ZNF556 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF556 MUTATED                              0                             1
  ZNF556 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF556 MUTATED                                               0
  ZNF556 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF556 MUTATED                              0
  ZNF556 WILD-TYPE                            9
D103V9, multiclass
                                                    clus
vv                                                   ZNF556 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF556 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V10, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     0  12
  ZNF556 WILD-TYPE  20 448
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      0   12
  ZNF556 WILD-TYPE   20  448
     clus
vv    ZNF556 MUTATED ZNF556 WILD-TYPE
  NO               0               20
  YES             12              448
[1] 2 2
[1] FALSE
D103V11, continuous
D103V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF556 MUTATED     6   2   0   0
  ZNF556 WILD-TYPE 304   9   4  25
D103V13, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  R0              6              304
  R1              2                9
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF556 MUTATED                                  0     0
  ZNF556 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF556 MUTATED                           1     9
  ZNF556 WILD-TYPE                        28   368
D103V14, multiclass
                                  clus
vv                                 ZNF556 MUTATED ZNF556 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V15, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     0   8
  ZNF556 WILD-TYPE   6 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      0    8
  ZNF556 WILD-TYPE    6  341
                        clus
vv                       ZNF556 MUTATED ZNF556 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              341
[1] 2 2
[1] FALSE

Clustering(104) Variable = ZEB1 MUTATION ANALYSIS
D104V1, survival
                sevent
clus2              0   1
  ZEB1 MUTATED    23   8
  ZEB1 WILD-TYPE 292 133
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            31            425 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
             8            133 
$`ZEB1 MUTATED`
TCGA-05-4250 TCGA-05-4424 TCGA-35-4123 TCGA-44-2656 TCGA-44-7662 TCGA-44-7671 
        3.98        30.02         5.98        46.98         7.17        17.59 
TCGA-49-6743 TCGA-50-5049 TCGA-55-1592 TCGA-55-7281 TCGA-55-7283 TCGA-55-8616 
       12.13        70.55        23.05         0.59         1.15         1.58 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-A46V TCGA-64-5774 TCGA-64-5779 TCGA-69-7761 
       20.19        19.99        72.30        87.98        28.41         6.12 
TCGA-69-7973 TCGA-69-8254 TCGA-73-4666 TCGA-78-7146 TCGA-78-7162 TCGA-78-8640 
        7.56        13.45        26.30         5.69       104.19       214.62 
TCGA-86-8585 TCGA-86-A456 TCGA-93-A4JO TCGA-97-7937 TCGA-MN-A4N4 TCGA-MP-A4T2 
        1.15        13.32         1.08         5.95        38.63        37.35 
TCGA-NJ-A4YI 
        0.13 

$`ZEB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
       19.46        12.03        36.07        18.87        29.00        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
        8.81        29.46        29.75        55.89        14.63        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       17.16        11.64        22.26        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7284 
       24.99        40.54       107.21        70.26         1.74         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         0.49         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       19.59         0.92        15.81         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       56.81        20.65        55.43        38.37         2.04        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64        13.87         6.64        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
        6.05         2.30         2.93        12.56        14.01         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       23.51       163.10        27.16        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 
        5.88        64.90        22.29         7.07       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        10.55        32.68        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       15.65        15.85        23.05        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
       30.84        27.58         0.62        14.96        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ 
        9.76         4.18         6.12        23.61        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81         0.20        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       14.10        19.13        73.91        71.05        62.60         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ZEB1 MUTATED ZEB1 WILD-TYPE 
          0.13           0.00 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
        214.62         223.96 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
         13.45          18.12 
[1] "0.1 - 214.6 (13.4)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D104V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZEB1 MUTATED         0       11       10         1         1          7
  ZEB1 WILD-TYPE       4      112      123        45        66         63
                vv
clus             STAGE IIIB STAGE IV
  ZEB1 MUTATED            0        1
  ZEB1 WILD-TYPE         11       24
D104V3, multiclass
            clus
vv           ZEB1 MUTATED ZEB1 WILD-TYPE
  STAGE I               0              4
  STAGE IA             11            112
  STAGE IB             10            123
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            7             63
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZEB1 MUTATED    12  17   3   0
  ZEB1 WILD-TYPE 143 244  40  18
D104V4, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  T1           12            143
  T2           17            244
  T3            3             40
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  ZEB1 MUTATED    23   2     6
  ZEB1 WILD-TYPE 284  87    66
D104V5, multiclass
       clus
vv      ZEB1 MUTATED ZEB1 WILD-TYPE
  N0              23            284
  N1               2             87
  N2+N3            6             66
[1] 3 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
  ZEB1 MUTATED    22   1
  ZEB1 WILD-TYPE 305  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     22    1
  ZEB1 WILD-TYPE  305   22
   clus
vv  ZEB1 MUTATED ZEB1 WILD-TYPE
  0           22            305
  1            1             22
[1] 2 2
[1] FALSE
D104V7, binary
                cls
clus               0   1
  ZEB1 MUTATED    12  20
  ZEB1 WILD-TYPE 247 201
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     12   20
  ZEB1 WILD-TYPE  247  201
        clus
vv       ZEB1 MUTATED ZEB1 WILD-TYPE
  FEMALE           12            247
  MALE             20            201
[1] 2 2
[1] FALSE
D104V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZEB1 MUTATED                            2                                 8
  ZEB1 WILD-TYPE                         16                                94
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZEB1 MUTATED                                                   16
  ZEB1 WILD-TYPE                                                278
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZEB1 MUTATED                                            0
  ZEB1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZEB1 MUTATED                                               1
  ZEB1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  ZEB1 MUTATED                                1
  ZEB1 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  ZEB1 MUTATED                                    1
  ZEB1 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZEB1 MUTATED                              0                             2
  ZEB1 WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZEB1 MUTATED                                               1
  ZEB1 WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  ZEB1 MUTATED                              0
  ZEB1 WILD-TYPE                            9
D104V9, multiclass
                                                    clus
vv                                                   ZEB1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           16
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   ZEB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            278
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V10, binary
                cls
clus               0   1
  ZEB1 MUTATED     3  29
  ZEB1 WILD-TYPE  17 431
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED      3   29
  ZEB1 WILD-TYPE   17  431
     clus
vv    ZEB1 MUTATED ZEB1 WILD-TYPE
  NO             3             17
  YES           29            431
[1] 2 2
[1] FALSE
D104V11, continuous
D104V12, continuous
                vv
clus              R0  R1  R2  RX
  ZEB1 MUTATED    18   1   1   1
  ZEB1 WILD-TYPE 292  10   3  24
D104V13, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  R0           18            292
  R1            1             10
  R2            1              3
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZEB1 MUTATED                                  0     1
  ZEB1 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZEB1 MUTATED                           1    26
  ZEB1 WILD-TYPE                        28   351
D104V14, multiclass
                                  clus
vv                                 ZEB1 MUTATED ZEB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      26            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V15, binary
                cls
clus               0   1
  ZEB1 MUTATED     0  23
  ZEB1 WILD-TYPE   6 326
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED      0   23
  ZEB1 WILD-TYPE    6  326
                        clus
vv                       ZEB1 MUTATED ZEB1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           23            326
[1] 2 2
[1] FALSE

Clustering(105) Variable = SLC22A6 MUTATION ANALYSIS
D105V1, survival
                   sevent
clus2                 0   1
  SLC22A6 MUTATED    12   2
  SLC22A6 WILD-TYPE 303 139
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               14               442 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
                2               139 
$`SLC22A6 MUTATED`
TCGA-05-4434 TCGA-35-4123 TCGA-44-2656 TCGA-44-6775 TCGA-55-5899 TCGA-55-7911 
       15.02         5.98        46.98        23.18         2.86        17.65 
TCGA-55-7994 TCGA-55-8510 TCGA-55-A4DG TCGA-64-1676 TCGA-67-3771 TCGA-86-8073 
       19.82        17.72        19.99        56.81        20.05        24.33 
TCGA-86-8672 TCGA-MN-A4N4 
        0.62        38.63 

$`SLC22A6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        0.53         6.48         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.49         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        20.19         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
             0.62              0.00 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
            56.81            223.96 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
           19.905            17.950 
[1] "0.6 - 56.8 (19.9)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.1"
D105V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC22A6 MUTATED         0        7        4         0         2          0
  SLC22A6 WILD-TYPE       4      116      129        46        65         70
                   vv
clus                STAGE IIIB STAGE IV
  SLC22A6 MUTATED            0        1
  SLC22A6 WILD-TYPE         11       24
D105V3, multiclass
            clus
vv           SLC22A6 MUTATED SLC22A6 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 7               116
  STAGE IB                 4               129
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of 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     7   4   2   1
  SLC22A6 WILD-TYPE 148 257  41  17
D105V4, multiclass
    clus
vv   SLC22A6 MUTATED SLC22A6 WILD-TYPE
  T1               7               148
  T2               4               257
  T3               2                41
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  SLC22A6 MUTATED    12   2     0
  SLC22A6 WILD-TYPE 295  87    72
D105V5, multiclass
       clus
vv      SLC22A6 MUTATED SLC22A6 WILD-TYPE
  N0                 12               295
  N1                  2                87
  N2+N3               0                72
[1] 3 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
  SLC22A6 MUTATED     8   1
  SLC22A6 WILD-TYPE 319  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      8    1
  SLC22A6 WILD-TYPE  319   22
   clus
vv  SLC22A6 MUTATED SLC22A6 WILD-TYPE
  0               8               319
  1               1                22
[1] 2 2
[1] FALSE
D105V7, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED     5   9
  SLC22A6 WILD-TYPE 254 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      5    9
  SLC22A6 WILD-TYPE  254  212
        clus
vv       SLC22A6 MUTATED SLC22A6 WILD-TYPE
  FEMALE               5               254
  MALE                 9               212
[1] 2 2
[1] FALSE
D105V8, continuous
[1] "Remove cluster labels:" "SLC22A6 MUTATED"       
clus
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-5375        TCGA-53-A4EZ        TCGA-55-7283 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7725        TCGA-55-7910        TCGA-55-7914 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-55-8089        TCGA-55-8096        TCGA-55-8205        TCGA-55-8208 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8511        TCGA-55-8512 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N5 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC22A6 MUTATED                            0
  SLC22A6 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC22A6 MUTATED                                   1
  SLC22A6 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC22A6 MUTATED                                                   12
  SLC22A6 WILD-TYPE                                                282
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC22A6 MUTATED                                            0
  SLC22A6 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC22A6 MUTATED                                               1
  SLC22A6 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC22A6 MUTATED                                0
  SLC22A6 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC22A6 MUTATED                                    0
  SLC22A6 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC22A6 MUTATED                              0                             0
  SLC22A6 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC22A6 MUTATED                                               0
  SLC22A6 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC22A6 MUTATED                              0
  SLC22A6 WILD-TYPE                            9
D105V9, multiclass
                                                    clus
vv                                                   SLC22A6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SLC22A6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V10, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED     0  14
  SLC22A6 WILD-TYPE  20 446
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      0   14
  SLC22A6 WILD-TYPE   20  446
     clus
vv    SLC22A6 MUTATED SLC22A6 WILD-TYPE
  NO                0                20
  YES              14               446
[1] 2 2
[1] FALSE
D105V11, continuous
D105V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC22A6 MUTATED    11   0   1   1
  SLC22A6 WILD-TYPE 299  11   3  24
D105V13, multiclass
    clus
vv   SLC22A6 MUTATED SLC22A6 WILD-TYPE
  R0              11               299
  R1               0                11
  R2               1                 3
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A6 MUTATED                                  0     0
  SLC22A6 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC22A6 MUTATED                           1    12
  SLC22A6 WILD-TYPE                        28   365
D105V14, multiclass
                                  clus
vv                                 SLC22A6 MUTATED SLC22A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                         12               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V15, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED     1  12
  SLC22A6 WILD-TYPE   5 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      1   12
  SLC22A6 WILD-TYPE    5  337
                        clus
vv                       SLC22A6 MUTATED SLC22A6 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              12               337
[1] 2 2
[1] FALSE

Clustering(106) Variable = RABEPK MUTATION ANALYSIS
D106V1, survival
                  sevent
clus2                0   1
  RABEPK MUTATED     2   4
  RABEPK WILD-TYPE 313 137
  RABEPK MUTATED RABEPK WILD-TYPE 
               6              450 
  RABEPK MUTATED RABEPK WILD-TYPE 
               4              137 
$`RABEPK MUTATED`
TCGA-44-6777 TCGA-55-6981 TCGA-78-7220 TCGA-91-6835 TCGA-L9-A444 TCGA-MP-A4TD 
       32.45        45.34        26.53         2.60         0.20        10.09 

$`RABEPK WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 
       48.49         3.88         5.49         7.79         2.20        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
      104.19       223.96         8.48        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
       26.47        10.62        41.36         1.97        10.19        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23         2.43        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  RABEPK MUTATED RABEPK WILD-TYPE 
             0.2              0.0 
  RABEPK MUTATED RABEPK WILD-TYPE 
           45.34           223.96 
  RABEPK MUTATED RABEPK WILD-TYPE 
           18.31            18.03 
[1] "0.2 - 45.3 (18.3)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.6"
D106V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RABEPK MUTATED         0        2        1         0         0          3
  RABEPK WILD-TYPE       4      121      132        46        67         67
                  vv
clus               STAGE IIIB STAGE IV
  RABEPK MUTATED            0        0
  RABEPK WILD-TYPE         11       25
D106V3, multiclass
            clus
vv           RABEPK MUTATED RABEPK WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                1              132
  STAGE IIA               0               46
  STAGE IIB               0               67
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RABEPK MUTATED     3   3   0   0
  RABEPK WILD-TYPE 152 258  43  18
D106V4, multiclass
    clus
vv   RABEPK MUTATED RABEPK WILD-TYPE
  T1              3              152
  T2              3              258
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  RABEPK MUTATED     2   0     3
  RABEPK WILD-TYPE 305  89    69
D106V5, multiclass
       clus
vv      RABEPK MUTATED RABEPK WILD-TYPE
  N0                 2              305
  N1                 0               89
  N2+N3              3               69
[1] 3 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
  RABEPK MUTATED     4   0
  RABEPK WILD-TYPE 323  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RABEPK MUTATED      4    0
  RABEPK WILD-TYPE  323   23
   clus
vv  RABEPK MUTATED RABEPK WILD-TYPE
  0              4              323
  1              0               23
[1] 2 2
[1] FALSE
D106V7, binary
                  cls
clus                 0   1
  RABEPK MUTATED     5   1
  RABEPK WILD-TYPE 254 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RABEPK MUTATED      5    1
  RABEPK WILD-TYPE  254  220
        clus
vv       RABEPK MUTATED RABEPK WILD-TYPE
  FEMALE              5              254
  MALE                1              220
[1] 2 2
[1] FALSE
D106V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RABEPK MUTATED                            0                                 1
  RABEPK WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RABEPK MUTATED                                                    5
  RABEPK WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RABEPK MUTATED                                            0
  RABEPK WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RABEPK MUTATED                                               0
  RABEPK WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  RABEPK MUTATED                                0
  RABEPK WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  RABEPK MUTATED                                    0
  RABEPK WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RABEPK MUTATED                              0                             0
  RABEPK WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RABEPK MUTATED                                               0
  RABEPK WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  RABEPK MUTATED                              0
  RABEPK WILD-TYPE                            9
D106V9, multiclass
                                                    clus
vv                                                   RABEPK MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   RABEPK WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V10, binary
                  cls
clus                 0   1
  RABEPK MUTATED     2   4
  RABEPK WILD-TYPE  18 456
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RABEPK MUTATED      2    4
  RABEPK WILD-TYPE   18  456
     clus
vv    RABEPK MUTATED RABEPK WILD-TYPE
  NO               2               18
  YES              4              456
[1] 2 2
[1] FALSE
D106V11, continuous
D106V12, continuous
                  vv
clus                R0  R1  R2  RX
  RABEPK MUTATED     4   0   0   1
  RABEPK WILD-TYPE 306  11   4  24
D106V13, multiclass
    clus
vv   RABEPK MUTATED RABEPK WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RABEPK MUTATED                                  0     0
  RABEPK WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RABEPK MUTATED                           0     6
  RABEPK WILD-TYPE                        29   371
D106V14, multiclass
                                  clus
vv                                 RABEPK MUTATED RABEPK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         6              371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V15, binary
                  cls
clus                 0   1
  RABEPK MUTATED     0   3
  RABEPK WILD-TYPE   6 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RABEPK MUTATED      0    3
  RABEPK WILD-TYPE    6  346
                        clus
vv                       RABEPK MUTATED RABEPK WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              3              346
[1] 2 2
[1] FALSE

Clustering(107) Variable = CHGB MUTATION ANALYSIS
D107V1, survival
                sevent
clus2              0   1
  CHGB MUTATED    11   3
  CHGB WILD-TYPE 304 138
  CHGB MUTATED CHGB WILD-TYPE 
            14            442 
  CHGB MUTATED CHGB WILD-TYPE 
             3            138 
$`CHGB MUTATED`
TCGA-38-4625 TCGA-44-3918 TCGA-44-8120 TCGA-50-6590 TCGA-53-A4EZ TCGA-55-7728 
       97.74        34.06         8.55        42.35         9.21         0.79 
TCGA-55-7911 TCGA-55-7994 TCGA-55-A4DF TCGA-69-7765 TCGA-73-4659 TCGA-95-7944 
       17.65        19.82        20.19         5.42        23.38        12.39 
TCGA-MN-A4N4 TCGA-MN-A4N5 
       38.63         2.76 

$`CHGB WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        22.55         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 
       27.25        34.29        30.54        13.94        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.48         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       27.19        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  CHGB MUTATED CHGB WILD-TYPE 
          0.79           0.00 
  CHGB MUTATED CHGB WILD-TYPE 
         97.74         223.96 
  CHGB MUTATED CHGB WILD-TYPE 
        18.735         18.030 
[1] "0.8 - 97.7 (18.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.5"
D107V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CHGB MUTATED         0        6        4         1         1          1
  CHGB WILD-TYPE       4      117      129        45        66         69
                vv
clus             STAGE IIIB STAGE IV
  CHGB MUTATED            0        1
  CHGB WILD-TYPE         11       24
D107V3, multiclass
            clus
vv           CHGB MUTATED CHGB WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              4            129
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHGB MUTATED     6   6   1   1
  CHGB WILD-TYPE 149 255  42  17
D107V4, multiclass
    clus
vv   CHGB MUTATED CHGB WILD-TYPE
  T1            6            149
  T2            6            255
  T3            1             42
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  CHGB MUTATED    12   1     1
  CHGB WILD-TYPE 295  88    71
D107V5, multiclass
       clus
vv      CHGB MUTATED CHGB WILD-TYPE
  N0              12            295
  N1               1             88
  N2+N3            1             71
[1] 3 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
  CHGB MUTATED     8   0
  CHGB WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED      8    0
  CHGB WILD-TYPE  319   23
   clus
vv  CHGB MUTATED CHGB WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D107V7, binary
                cls
clus               0   1
  CHGB MUTATED     5   9
  CHGB WILD-TYPE 254 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED      5    9
  CHGB WILD-TYPE  254  212
        clus
vv       CHGB MUTATED CHGB WILD-TYPE
  FEMALE            5            254
  MALE              9            212
[1] 2 2
[1] FALSE
D107V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHGB MUTATED                            1                                 1
  CHGB WILD-TYPE                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHGB MUTATED                                                   11
  CHGB WILD-TYPE                                                283
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CHGB MUTATED                                            0
  CHGB WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CHGB MUTATED                                               0
  CHGB WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  CHGB MUTATED                                0
  CHGB WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  CHGB MUTATED                                    0
  CHGB WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CHGB MUTATED                              0                             0
  CHGB WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CHGB MUTATED                                               0
  CHGB WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  CHGB MUTATED                              1
  CHGB WILD-TYPE                            8
D107V9, multiclass
                                                    clus
vv                                                   CHGB MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   CHGB WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V10, binary
                cls
clus               0   1
  CHGB MUTATED     0  14
  CHGB WILD-TYPE  20 446
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED      0   14
  CHGB WILD-TYPE   20  446
     clus
vv    CHGB MUTATED CHGB WILD-TYPE
  NO             0             20
  YES           14            446
[1] 2 2
[1] FALSE
D107V11, continuous
D107V12, continuous
                vv
clus              R0  R1  R2  RX
  CHGB MUTATED    10   0   0   1
  CHGB WILD-TYPE 300  11   4  24
D107V13, multiclass
    clus
vv   CHGB MUTATED CHGB WILD-TYPE
  R0           10            300
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHGB MUTATED                                  0     0
  CHGB WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHGB MUTATED                           2    11
  CHGB WILD-TYPE                        27   366
D107V14, multiclass
                                  clus
vv                                 CHGB MUTATED CHGB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                      11            366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V15, binary
                cls
clus               0   1
  CHGB MUTATED     1  12
  CHGB WILD-TYPE   5 337
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED      1   12
  CHGB WILD-TYPE    5  337
                        clus
vv                       CHGB MUTATED CHGB WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           12            337
[1] 2 2
[1] FALSE

Clustering(108) Variable = ESYT3 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2               0   1
  ESYT3 MUTATED     6   2
  ESYT3 WILD-TYPE 309 139
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             448 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              2             139 
$`ESYT3 MUTATED`
TCGA-05-4397 TCGA-05-5425 TCGA-38-7271 TCGA-44-7661 TCGA-55-8089 TCGA-55-8506 
       24.03        29.00        26.30        12.03         3.29         0.36 
TCGA-62-A46U TCGA-91-6849 
       67.96         1.15 

$`ESYT3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       14.60        19.46         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ESYT3 MUTATED ESYT3 WILD-TYPE 
           0.36            0.00 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
          67.96          223.96 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
          18.03           18.03 
[1] "0.4 - 68.0 (18.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D108V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ESYT3 MUTATED         0        2        1         0         4          1
  ESYT3 WILD-TYPE       4      121      132        46        63         69
                 vv
clus              STAGE IIIB STAGE IV
  ESYT3 MUTATED            0        0
  ESYT3 WILD-TYPE         11       25
D108V3, multiclass
            clus
vv           ESYT3 MUTATED ESYT3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               1             132
  STAGE IIA              0              46
  STAGE IIB              4              63
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESYT3 MUTATED     2   5   1   0
  ESYT3 WILD-TYPE 153 256  42  18
D108V4, multiclass
    clus
vv   ESYT3 MUTATED ESYT3 WILD-TYPE
  T1             2             153
  T2             5             256
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ESYT3 MUTATED     4   3     1
  ESYT3 WILD-TYPE 303  86    71
D108V5, multiclass
       clus
vv      ESYT3 MUTATED ESYT3 WILD-TYPE
  N0                4             303
  N1                3              86
  N2+N3             1              71
[1] 3 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
  ESYT3 MUTATED     6   0
  ESYT3 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      6    0
  ESYT3 WILD-TYPE  321   23
   clus
vv  ESYT3 MUTATED ESYT3 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D108V7, binary
                 cls
clus                0   1
  ESYT3 MUTATED     5   3
  ESYT3 WILD-TYPE 254 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      5    3
  ESYT3 WILD-TYPE  254  218
        clus
vv       ESYT3 MUTATED ESYT3 WILD-TYPE
  FEMALE             5             254
  MALE               3             218
[1] 2 2
[1] FALSE
D108V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ESYT3 MUTATED                            0                                 3
  ESYT3 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ESYT3 MUTATED                                                    5
  ESYT3 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ESYT3 MUTATED                                            0
  ESYT3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ESYT3 MUTATED                                               0
  ESYT3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ESYT3 MUTATED                                0
  ESYT3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ESYT3 MUTATED                                    0
  ESYT3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ESYT3 MUTATED                              0                             0
  ESYT3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ESYT3 MUTATED                                               0
  ESYT3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ESYT3 MUTATED                              0
  ESYT3 WILD-TYPE                            9
D108V9, multiclass
                                                    clus
vv                                                   ESYT3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ESYT3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V10, binary
                 cls
clus                0   1
  ESYT3 MUTATED     0   8
  ESYT3 WILD-TYPE  20 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      0    8
  ESYT3 WILD-TYPE   20  452
     clus
vv    ESYT3 MUTATED ESYT3 WILD-TYPE
  NO              0              20
  YES             8             452
[1] 2 2
[1] FALSE
D108V11, continuous
D108V12, continuous
                 vv
clus               R0  R1  R2  RX
  ESYT3 MUTATED     6   0   0   0
  ESYT3 WILD-TYPE 304  11   4  25
D108V13, multiclass
    clus
vv   ESYT3 MUTATED ESYT3 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESYT3 MUTATED                                  0     0
  ESYT3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESYT3 MUTATED                           1     5
  ESYT3 WILD-TYPE                        28   372
D108V14, multiclass
                                  clus
vv                                 ESYT3 MUTATED ESYT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V15, binary
                 cls
clus                0   1
  ESYT3 MUTATED     0   6
  ESYT3 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      0    6
  ESYT3 WILD-TYPE    6  343
                        clus
vv                       ESYT3 MUTATED ESYT3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(109) Variable = L1CAM MUTATION ANALYSIS
D109V1, survival
                 sevent
clus2               0   1
  L1CAM MUTATED    23   9
  L1CAM WILD-TYPE 292 132
  L1CAM MUTATED L1CAM WILD-TYPE 
             32             424 
  L1CAM MUTATED L1CAM WILD-TYPE 
              9             132 
$`L1CAM MUTATED`
TCGA-05-4405 TCGA-05-4427 TCGA-44-3918 TCGA-44-4112 TCGA-44-6776 TCGA-44-7670 
       20.05        26.01        34.06        26.56        63.72        29.00 
TCGA-44-8119 TCGA-49-6743 TCGA-50-5946 TCGA-50-6594 TCGA-55-1592 TCGA-55-6970 
        3.25        12.13        22.55        12.16        23.05        15.25 
TCGA-55-7281 TCGA-55-7911 TCGA-55-8299 TCGA-55-8506 TCGA-55-8510 TCGA-55-A48X 
        0.59        17.65        15.42         0.36        17.72        22.65 
TCGA-55-A492 TCGA-64-5781 TCGA-78-7160 TCGA-78-7220 TCGA-78-7537 TCGA-78-8662 
       19.59        51.25        22.29        26.53        53.33       110.50 
TCGA-86-7701 TCGA-91-6836 TCGA-95-7039 TCGA-97-7546 TCGA-97-7547 TCGA-99-8028 
       31.13        13.71         1.12        31.69        64.60        36.76 
TCGA-J2-A4AG TCGA-MP-A4T4 
       16.44        86.04 

$`L1CAM WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       37.15        38.24         6.25        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
       12.03         7.17        36.07        18.87        17.59        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
       29.46        29.75        55.89        14.63        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 
       27.25        34.29        30.54        13.94         9.21        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       70.26         1.74         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 
       17.98         1.08         1.51         2.17        22.16         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
        0.76         0.95         0.26         0.49         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        16.93        20.71        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        42.90        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        64.90         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
      223.96         8.48        88.14        31.20         8.02        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
       10.55        27.09        12.36         5.88        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       35.47        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  L1CAM MUTATED L1CAM WILD-TYPE 
           0.36            0.00 
  L1CAM MUTATED L1CAM WILD-TYPE 
         110.50          223.96 
  L1CAM MUTATED L1CAM WILD-TYPE 
          22.60           17.62 
[1] "0.4 - 110.5 (22.6)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.5"
D109V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  L1CAM MUTATED         0       11        9         3         5          4
  L1CAM WILD-TYPE       4      112      124        43        62         66
                 vv
clus              STAGE IIIB STAGE IV
  L1CAM MUTATED            0        2
  L1CAM WILD-TYPE         11       23
D109V3, multiclass
            clus
vv           L1CAM MUTATED L1CAM WILD-TYPE
  STAGE I                0               4
  STAGE IA              11             112
  STAGE IB               9             124
  STAGE IIA              3              43
  STAGE IIB              5              62
  STAGE IIIA             4              66
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  L1CAM MUTATED    13  16   4   1
  L1CAM WILD-TYPE 142 245  39  17
D109V4, multiclass
    clus
vv   L1CAM MUTATED L1CAM WILD-TYPE
  T1            13             142
  T2            16             245
  T3             4              39
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  L1CAM MUTATED    24   5     5
  L1CAM WILD-TYPE 283  84    67
D109V5, multiclass
       clus
vv      L1CAM MUTATED L1CAM WILD-TYPE
  N0               24             283
  N1                5              84
  N2+N3             5              67
[1] 3 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
  L1CAM MUTATED    18   2
  L1CAM WILD-TYPE 309  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED     18    2
  L1CAM WILD-TYPE  309   21
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0            18             309
  1             2              21
[1] 2 2
[1] FALSE
D109V7, binary
                 cls
clus                0   1
  L1CAM MUTATED    27   7
  L1CAM WILD-TYPE 232 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED     27    7
  L1CAM WILD-TYPE  232  214
        clus
vv       L1CAM MUTATED L1CAM WILD-TYPE
  FEMALE            27             232
  MALE               7             214
[1] 2 2
[1] FALSE
D109V8, continuous
[1] "Remove cluster labels:" "L1CAM MUTATED"         
clus
  L1CAM MUTATED L1CAM WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7711      TCGA-86-7713 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  L1CAM MUTATED                            1                                 9
  L1CAM WILD-TYPE                         17                                93
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  L1CAM MUTATED                                                   20
  L1CAM WILD-TYPE                                                274
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  L1CAM MUTATED                                            0
  L1CAM WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  L1CAM MUTATED                                               0
  L1CAM WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  L1CAM MUTATED                                1
  L1CAM WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  L1CAM MUTATED                                    1
  L1CAM WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  L1CAM MUTATED                              0                             2
  L1CAM WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  L1CAM MUTATED                                               0
  L1CAM WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  L1CAM MUTATED                              0
  L1CAM WILD-TYPE                            9
D109V9, multiclass
                                                    clus
vv                                                   L1CAM MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            20
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   L1CAM WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             274
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V10, binary
                 cls
clus                0   1
  L1CAM MUTATED     1  33
  L1CAM WILD-TYPE  19 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      1   33
  L1CAM WILD-TYPE   19  427
     clus
vv    L1CAM MUTATED L1CAM WILD-TYPE
  NO              1              19
  YES            33             427
[1] 2 2
[1] FALSE
D109V11, continuous
D109V12, continuous
                 vv
clus               R0  R1  R2  RX
  L1CAM MUTATED    23   1   0   1
  L1CAM WILD-TYPE 287  10   4  24
D109V13, multiclass
    clus
vv   L1CAM MUTATED L1CAM WILD-TYPE
  R0            23             287
  R1             1              10
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  L1CAM MUTATED                                  0     0
  L1CAM WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  L1CAM MUTATED                           2    26
  L1CAM WILD-TYPE                        27   351
D109V14, multiclass
                                  clus
vv                                 L1CAM MUTATED L1CAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       26             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V15, binary
                 cls
clus                0   1
  L1CAM MUTATED     1  19
  L1CAM WILD-TYPE   5 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      1   19
  L1CAM WILD-TYPE    5  330
                        clus
vv                       L1CAM MUTATED L1CAM WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            19             330
[1] 2 2
[1] FALSE

Clustering(110) Variable = SLC17A3 MUTATION ANALYSIS
D110V1, survival
                   sevent
clus2                 0   1
  SLC17A3 MUTATED     9   5
  SLC17A3 WILD-TYPE 306 136
  SLC17A3 MUTATED SLC17A3 WILD-TYPE 
               14               442 
  SLC17A3 MUTATED SLC17A3 WILD-TYPE 
                5               136 
$`SLC17A3 MUTATED`
TCGA-05-4420 TCGA-05-5425 TCGA-44-6777 TCGA-44-6778 TCGA-44-7669 TCGA-49-4514 
       29.98        29.00        32.45        61.28        18.87        55.89 
TCGA-50-5049 TCGA-50-6590 TCGA-55-8205 TCGA-62-A46O TCGA-64-5815 TCGA-78-7155 
       70.55        42.35         1.08        47.80        28.47        38.50 
TCGA-86-7955 TCGA-MN-A4N4 
       16.70        38.63 

$`SLC17A3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        23.18        63.72        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03         7.17        36.07        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       32.84         8.81        29.46        29.75        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       13.87        20.55        19.43        19.89        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SLC17A3 MUTATED SLC17A3 WILD-TYPE 
             1.08              0.00 
  SLC17A3 MUTATED SLC17A3 WILD-TYPE 
            70.55            223.96 
  SLC17A3 MUTATED SLC17A3 WILD-TYPE 
           35.475            17.635 
[1] "1.1 - 70.5 (35.5)"  "0.0 - 224.0 (17.6)"
[1] "hr=" "1.5"
D110V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC17A3 MUTATED         0        4        6         1         3          1
  SLC17A3 WILD-TYPE       4      119      127        45        64         69
                   vv
clus                STAGE IIIB STAGE IV
  SLC17A3 MUTATED            0        0
  SLC17A3 WILD-TYPE         11       25
D110V3, multiclass
            clus
vv           SLC17A3 MUTATED SLC17A3 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 4               119
  STAGE IB                 6               127
  STAGE IIA                1                45
  STAGE IIB                3                64
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC17A3 MUTATED     4  11   0   0
  SLC17A3 WILD-TYPE 151 250  43  18
D110V4, multiclass
    clus
vv   SLC17A3 MUTATED SLC17A3 WILD-TYPE
  T1               4               151
  T2              11               250
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  SLC17A3 MUTATED    10   3     1
  SLC17A3 WILD-TYPE 297  86    71
D110V5, multiclass
       clus
vv      SLC17A3 MUTATED SLC17A3 WILD-TYPE
  N0                 10               297
  N1                  3                86
  N2+N3               1                71
[1] 3 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
  SLC17A3 MUTATED    12   0
  SLC17A3 WILD-TYPE 315  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A3 MUTATED     12    0
  SLC17A3 WILD-TYPE  315   23
   clus
vv  SLC17A3 MUTATED SLC17A3 WILD-TYPE
  0              12               315
  1               0                23
[1] 2 2
[1] FALSE
D110V7, binary
                   cls
clus                  0   1
  SLC17A3 MUTATED     6   9
  SLC17A3 WILD-TYPE 253 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A3 MUTATED      6    9
  SLC17A3 WILD-TYPE  253  212
        clus
vv       SLC17A3 MUTATED SLC17A3 WILD-TYPE
  FEMALE               6               253
  MALE                 9               212
[1] 2 2
[1] FALSE
D110V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC17A3 MUTATED                            0
  SLC17A3 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC17A3 MUTATED                                   3
  SLC17A3 WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC17A3 MUTATED                                                   11
  SLC17A3 WILD-TYPE                                                283
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC17A3 MUTATED                                            0
  SLC17A3 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC17A3 MUTATED                                               0
  SLC17A3 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC17A3 MUTATED                                0
  SLC17A3 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC17A3 MUTATED                                    0
  SLC17A3 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC17A3 MUTATED                              0                             1
  SLC17A3 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC17A3 MUTATED                                               0
  SLC17A3 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC17A3 MUTATED                              0
  SLC17A3 WILD-TYPE                            9
D110V9, multiclass
                                                    clus
vv                                                   SLC17A3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SLC17A3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V10, binary
                   cls
clus                  0   1
  SLC17A3 MUTATED     2  13
  SLC17A3 WILD-TYPE  18 447
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A3 MUTATED      2   13
  SLC17A3 WILD-TYPE   18  447
     clus
vv    SLC17A3 MUTATED SLC17A3 WILD-TYPE
  NO                2                18
  YES              13               447
[1] 2 2
[1] FALSE
D110V11, continuous
D110V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC17A3 MUTATED     9   0   0   1
  SLC17A3 WILD-TYPE 301  11   4  24
D110V13, multiclass
    clus
vv   SLC17A3 MUTATED SLC17A3 WILD-TYPE
  R0               9               301
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC17A3 MUTATED                                  0     0
  SLC17A3 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC17A3 MUTATED                           2    10
  SLC17A3 WILD-TYPE                        27   367
D110V14, multiclass
                                  clus
vv                                 SLC17A3 MUTATED SLC17A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         10               367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V15, binary
                   cls
clus                  0   1
  SLC17A3 MUTATED     0   8
  SLC17A3 WILD-TYPE   6 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A3 MUTATED      0    8
  SLC17A3 WILD-TYPE    6  341
                        clus
vv                       SLC17A3 MUTATED SLC17A3 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               8               341
[1] 2 2
[1] FALSE

Clustering(111) Variable = ITIH2 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2               0   1
  ITIH2 MUTATED    11   5
  ITIH2 WILD-TYPE 304 136
  ITIH2 MUTATED ITIH2 WILD-TYPE 
             16             440 
  ITIH2 MUTATED ITIH2 WILD-TYPE 
              5             136 
$`ITIH2 MUTATED`
TCGA-05-4249 TCGA-05-5425 TCGA-35-4122 TCGA-44-2656 TCGA-44-6778 TCGA-50-5930 
       50.07        29.00         7.40        46.98        61.28         9.27 
TCGA-50-6592 TCGA-55-8092 TCGA-55-8616 TCGA-55-A490 TCGA-55-A493 TCGA-78-7536 
       25.55         5.06         1.58         1.58         0.92         8.02 
TCGA-86-6851 TCGA-86-8073 TCGA-86-8674 TCGA-MP-A4SY 
        5.88        24.33        13.32        49.35 

$`ITIH2 WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        32.45        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        8.22        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
        3.29        19.66        19.73         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       21.40        20.58        19.59        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53        31.20        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
       27.58         0.62        14.96        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ITIH2 MUTATED ITIH2 WILD-TYPE 
           0.92            0.00 
  ITIH2 MUTATED ITIH2 WILD-TYPE 
          61.28          223.96 
  ITIH2 MUTATED ITIH2 WILD-TYPE 
         11.295          18.100 
[1] "0.9 - 61.3 (11.3)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D111V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ITIH2 MUTATED         0        2        6         3         4          4
  ITIH2 WILD-TYPE       4      121      127        43        63         66
                 vv
clus              STAGE IIIB STAGE IV
  ITIH2 MUTATED            0        0
  ITIH2 WILD-TYPE         11       25
D111V3, multiclass
            clus
vv           ITIH2 MUTATED ITIH2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               6             127
  STAGE IIA              3              43
  STAGE IIB              4              63
  STAGE IIIA             4              66
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITIH2 MUTATED     3  14   2   0
  ITIH2 WILD-TYPE 152 247  41  18
D111V4, multiclass
    clus
vv   ITIH2 MUTATED ITIH2 WILD-TYPE
  T1             3             152
  T2            14             247
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ITIH2 MUTATED    10   5     4
  ITIH2 WILD-TYPE 297  84    68
D111V5, multiclass
       clus
vv      ITIH2 MUTATED ITIH2 WILD-TYPE
  N0               10             297
  N1                5              84
  N2+N3             4              68
[1] 3 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
  ITIH2 MUTATED    16   0
  ITIH2 WILD-TYPE 311  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITIH2 MUTATED     16    0
  ITIH2 WILD-TYPE  311   23
   clus
vv  ITIH2 MUTATED ITIH2 WILD-TYPE
  0            16             311
  1             0              23
[1] 2 2
[1] FALSE
D111V7, binary
                 cls
clus                0   1
  ITIH2 MUTATED     6  13
  ITIH2 WILD-TYPE 253 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITIH2 MUTATED      6   13
  ITIH2 WILD-TYPE  253  208
        clus
vv       ITIH2 MUTATED ITIH2 WILD-TYPE
  FEMALE             6             253
  MALE              13             208
[1] 2 2
[1] FALSE
D111V8, continuous
[1] "Remove cluster labels:" "ITIH2 MUTATED"         
clus
  ITIH2 MUTATED ITIH2 WILD-TYPE 
              2              82 
     TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ      TCGA-55-7283 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A494 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"ITIH2 WILD-TYPE" "ITIH2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ITIH2 MUTATED                            0                                 3
  ITIH2 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ITIH2 MUTATED                                                   13
  ITIH2 WILD-TYPE                                                281
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ITIH2 MUTATED                                            0
  ITIH2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ITIH2 MUTATED                                               1
  ITIH2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ITIH2 MUTATED                                0
  ITIH2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ITIH2 MUTATED                                    0
  ITIH2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ITIH2 MUTATED                              0                             2
  ITIH2 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ITIH2 MUTATED                                               0
  ITIH2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ITIH2 MUTATED                              0
  ITIH2 WILD-TYPE                            9
D111V9, multiclass
                                                    clus
vv                                                   ITIH2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ITIH2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V10, binary
                 cls
clus                0   1
  ITIH2 MUTATED     2  17
  ITIH2 WILD-TYPE  18 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITIH2 MUTATED      2   17
  ITIH2 WILD-TYPE   18  443
     clus
vv    ITIH2 MUTATED ITIH2 WILD-TYPE
  NO              2              18
  YES            17             443
[1] 2 2
[1] FALSE
D111V11, continuous
D111V12, continuous
                 vv
clus               R0  R1  R2  RX
  ITIH2 MUTATED    13   0   1   0
  ITIH2 WILD-TYPE 297  11   3  25
D111V13, multiclass
    clus
vv   ITIH2 MUTATED ITIH2 WILD-TYPE
  R0            13             297
  R1             0              11
  R2             1               3
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITIH2 MUTATED                                  0     0
  ITIH2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITIH2 MUTATED                           1    13
  ITIH2 WILD-TYPE                        28   364
D111V14, multiclass
                                  clus
vv                                 ITIH2 MUTATED ITIH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       13             364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V15, binary
                 cls
clus                0   1
  ITIH2 MUTATED     0  12
  ITIH2 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITIH2 MUTATED      0   12
  ITIH2 WILD-TYPE    6  337
                        clus
vv                       ITIH2 MUTATED ITIH2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(112) Variable = HP1BP3 MUTATION ANALYSIS
D112V1, survival
                  sevent
clus2                0   1
  HP1BP3 MUTATED     6   1
  HP1BP3 WILD-TYPE 309 140
  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
               7              449 
  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
               1              140 
$`HP1BP3 MUTATED`
TCGA-05-4420 TCGA-05-4432 TCGA-44-2656 TCGA-55-8092 TCGA-55-A490 TCGA-64-5781 
       29.98        25.02        46.98         5.06         1.58        51.25 
TCGA-86-6851 
        5.88 

$`HP1BP3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
            1.58             0.00 
  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
           51.25           223.96 
  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
           25.02            17.98 
[1] "1.6 - 51.2 (25.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.4"
D112V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HP1BP3 MUTATED         0        1        3         2         2          0
  HP1BP3 WILD-TYPE       4      122      130        44        65         70
                  vv
clus               STAGE IIIB STAGE IV
  HP1BP3 MUTATED            0        0
  HP1BP3 WILD-TYPE         11       25
D112V3, multiclass
            clus
vv           HP1BP3 MUTATED HP1BP3 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                3              130
  STAGE IIA               2               44
  STAGE IIB               2               65
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HP1BP3 MUTATED     2   5   1   0
  HP1BP3 WILD-TYPE 153 256  42  18
D112V4, multiclass
    clus
vv   HP1BP3 MUTATED HP1BP3 WILD-TYPE
  T1              2              153
  T2              5              256
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  HP1BP3 MUTATED     6   2     0
  HP1BP3 WILD-TYPE 301  87    72
D112V5, multiclass
       clus
vv      HP1BP3 MUTATED HP1BP3 WILD-TYPE
  N0                 6              301
  N1                 2               87
  N2+N3              0               72
[1] 3 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
  HP1BP3 MUTATED     6   0
  HP1BP3 WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HP1BP3 MUTATED      6    0
  HP1BP3 WILD-TYPE  321   23
   clus
vv  HP1BP3 MUTATED HP1BP3 WILD-TYPE
  0              6              321
  1              0               23
[1] 2 2
[1] FALSE
D112V7, binary
                  cls
clus                 0   1
  HP1BP3 MUTATED     3   5
  HP1BP3 WILD-TYPE 256 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HP1BP3 MUTATED      3    5
  HP1BP3 WILD-TYPE  256  216
        clus
vv       HP1BP3 MUTATED HP1BP3 WILD-TYPE
  FEMALE              3              256
  MALE                5              216
[1] 2 2
[1] FALSE
D112V8, continuous
[1] "Remove cluster labels:" "HP1BP3 MUTATED"        
clus
  HP1BP3 MUTATED HP1BP3 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" "HP1BP3 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HP1BP3 MUTATED                            0                                 4
  HP1BP3 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HP1BP3 MUTATED                                                    4
  HP1BP3 WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HP1BP3 MUTATED                                            0
  HP1BP3 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HP1BP3 MUTATED                                               0
  HP1BP3 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  HP1BP3 MUTATED                                0
  HP1BP3 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  HP1BP3 MUTATED                                    0
  HP1BP3 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HP1BP3 MUTATED                              0                             0
  HP1BP3 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HP1BP3 MUTATED                                               0
  HP1BP3 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  HP1BP3 MUTATED                              0
  HP1BP3 WILD-TYPE                            9
D112V9, multiclass
                                                    clus
vv                                                   HP1BP3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   HP1BP3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V10, binary
                  cls
clus                 0   1
  HP1BP3 MUTATED     0   8
  HP1BP3 WILD-TYPE  20 452
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HP1BP3 MUTATED      0    8
  HP1BP3 WILD-TYPE   20  452
     clus
vv    HP1BP3 MUTATED HP1BP3 WILD-TYPE
  NO               0               20
  YES              8              452
[1] 2 2
[1] FALSE
D112V11, continuous
D112V12, continuous
                  vv
clus                R0  R1  R2  RX
  HP1BP3 MUTATED     6   0   0   0
  HP1BP3 WILD-TYPE 304  11   4  25
D112V13, multiclass
    clus
vv   HP1BP3 MUTATED HP1BP3 WILD-TYPE
  R0              6              304
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HP1BP3 MUTATED                                  0     0
  HP1BP3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HP1BP3 MUTATED                           0     5
  HP1BP3 WILD-TYPE                        29   372
D112V14, multiclass
                                  clus
vv                                 HP1BP3 MUTATED HP1BP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V15, binary
                  cls
clus                 0   1
  HP1BP3 MUTATED     0   5
  HP1BP3 WILD-TYPE   6 344
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HP1BP3 MUTATED      0    5
  HP1BP3 WILD-TYPE    6  344
                        clus
vv                       HP1BP3 MUTATED HP1BP3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              344
[1] 2 2
[1] FALSE

Clustering(113) Variable = LAMA4 MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2               0   1
  LAMA4 MUTATED    24   6
  LAMA4 WILD-TYPE 291 135
  LAMA4 MUTATED LAMA4 WILD-TYPE 
             30             426 
  LAMA4 MUTATED LAMA4 WILD-TYPE 
              6             135 
$`LAMA4 MUTATED`
TCGA-05-4382 TCGA-05-4398 TCGA-38-4625 TCGA-44-7660 TCGA-44-8119 TCGA-49-6767 
       19.96        47.05        97.74        19.46         3.25        22.26 
TCGA-50-5931 TCGA-50-5946 TCGA-53-A4EZ TCGA-55-5899 TCGA-62-A46O TCGA-64-5778 
       14.27        22.55         9.21         2.86        47.80        42.90 
TCGA-78-7161 TCGA-78-7220 TCGA-78-8662 TCGA-86-8073 TCGA-86-8674 TCGA-91-6836 
        7.07        26.53       110.50        24.33        13.32        13.71 
TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VP TCGA-97-A4M3 TCGA-99-7458 TCGA-99-8032 
        1.22        15.68        19.89        17.75        24.56         1.45 
TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-NJ-A4YQ 
       18.08         3.81         0.20        38.63        86.14        29.13 

$`LAMA4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       14.60        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 
       12.13        29.26        17.16        11.64        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       55.43        38.37        87.98         2.04        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
       22.29       104.19       223.96         8.48        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      214.62        39.75        77.59        10.55        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.12         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        20.84        18.67        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
       34.85        36.76         5.59        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW 
       16.44        19.00        14.30        27.19         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  LAMA4 MUTATED LAMA4 WILD-TYPE 
            0.2             0.0 
  LAMA4 MUTATED LAMA4 WILD-TYPE 
         110.50          223.96 
  LAMA4 MUTATED LAMA4 WILD-TYPE 
         19.675          17.820 
[1] "0.2 - 110.5 (19.7)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.9"
D113V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LAMA4 MUTATED         0       12       12         2         3          3
  LAMA4 WILD-TYPE       4      111      121        44        64         67
                 vv
clus              STAGE IIIB STAGE IV
  LAMA4 MUTATED            1        1
  LAMA4 WILD-TYPE         10       24
D113V3, multiclass
            clus
vv           LAMA4 MUTATED LAMA4 WILD-TYPE
  STAGE I                0               4
  STAGE IA              12             111
  STAGE IB              12             121
  STAGE IIA              2              44
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAMA4 MUTATED    12  17   3   2
  LAMA4 WILD-TYPE 143 244  40  16
D113V4, multiclass
    clus
vv   LAMA4 MUTATED LAMA4 WILD-TYPE
  T1            12             143
  T2            17             244
  T3             3              40
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  LAMA4 MUTATED    26   3     4
  LAMA4 WILD-TYPE 281  86    68
D113V5, multiclass
       clus
vv      LAMA4 MUTATED LAMA4 WILD-TYPE
  N0               26             281
  N1                3              86
  N2+N3             4              68
[1] 3 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
  LAMA4 MUTATED    24   1
  LAMA4 WILD-TYPE 303  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA4 MUTATED     24    1
  LAMA4 WILD-TYPE  303   22
   clus
vv  LAMA4 MUTATED LAMA4 WILD-TYPE
  0            24             303
  1             1              22
[1] 2 2
[1] FALSE
D113V7, binary
                 cls
clus                0   1
  LAMA4 MUTATED    17  17
  LAMA4 WILD-TYPE 242 204
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA4 MUTATED     17   17
  LAMA4 WILD-TYPE  242  204
        clus
vv       LAMA4 MUTATED LAMA4 WILD-TYPE
  FEMALE            17             242
  MALE              17             204
[1] 2 2
[1] FALSE
D113V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LAMA4 MUTATED                            2                                 9
  LAMA4 WILD-TYPE                         16                                93
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LAMA4 MUTATED                                                   19
  LAMA4 WILD-TYPE                                                275
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LAMA4 MUTATED                                            0
  LAMA4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LAMA4 MUTATED                                               3
  LAMA4 WILD-TYPE                                            16
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  LAMA4 MUTATED                                0
  LAMA4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  LAMA4 MUTATED                                    0
  LAMA4 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LAMA4 MUTATED                              0                             1
  LAMA4 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LAMA4 MUTATED                                               0
  LAMA4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  LAMA4 MUTATED                              0
  LAMA4 WILD-TYPE                            9
D113V9, multiclass
                                                    clus
vv                                                   LAMA4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   LAMA4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             275
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V10, binary
                 cls
clus                0   1
  LAMA4 MUTATED     1  33
  LAMA4 WILD-TYPE  19 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA4 MUTATED      1   33
  LAMA4 WILD-TYPE   19  427
     clus
vv    LAMA4 MUTATED LAMA4 WILD-TYPE
  NO              1              19
  YES            33             427
[1] 2 2
[1] FALSE
D113V11, continuous
D113V12, continuous
                 vv
clus               R0  R1  R2  RX
  LAMA4 MUTATED    20   1   0   5
  LAMA4 WILD-TYPE 290  10   4  20
D113V13, multiclass
    clus
vv   LAMA4 MUTATED LAMA4 WILD-TYPE
  R0            20             290
  R1             1              10
  R2             0               4
  RX             5              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAMA4 MUTATED                                  0     0
  LAMA4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAMA4 MUTATED                           0    27
  LAMA4 WILD-TYPE                        29   350
D113V14, multiclass
                                  clus
vv                                 LAMA4 MUTATED LAMA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       27             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V15, binary
                 cls
clus                0   1
  LAMA4 MUTATED     1  21
  LAMA4 WILD-TYPE   5 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA4 MUTATED      1   21
  LAMA4 WILD-TYPE    5  328
                        clus
vv                       LAMA4 MUTATED LAMA4 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            21             328
[1] 2 2
[1] FALSE

Clustering(114) Variable = TMCO2 MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  TMCO2 MUTATED     4   2
  TMCO2 WILD-TYPE 311 139
  TMCO2 MUTATED TMCO2 WILD-TYPE 
              6             450 
  TMCO2 MUTATED TMCO2 WILD-TYPE 
              2             139 
$`TMCO2 MUTATED`
TCGA-50-6594 TCGA-55-8506 TCGA-55-8508 TCGA-69-7978 TCGA-78-7536 TCGA-95-7947 
       12.16         0.36         0.49         2.30         8.02        15.68 

$`TMCO2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        11.05         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
       15.42         1.45         0.76         0.95         0.26        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        26.53        31.20        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  TMCO2 MUTATED TMCO2 WILD-TYPE 
           0.36            0.00 
  TMCO2 MUTATED TMCO2 WILD-TYPE 
          15.68          223.96 
  TMCO2 MUTATED TMCO2 WILD-TYPE 
           5.16           18.41 
[1] "0.4 - 15.7 (5.2)"   "0.0 - 224.0 (18.4)"
[1] "hr=" "5"  
D114V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TMCO2 MUTATED         0        1        0         1         2          2
  TMCO2 WILD-TYPE       4      122      133        45        65         68
                 vv
clus              STAGE IIIB STAGE IV
  TMCO2 MUTATED            0        0
  TMCO2 WILD-TYPE         11       25
D114V3, multiclass
            clus
vv           TMCO2 MUTATED TMCO2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               0             133
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TMCO2 MUTATED     1   3   2   0
  TMCO2 WILD-TYPE 154 258  41  18
D114V4, multiclass
    clus
vv   TMCO2 MUTATED TMCO2 WILD-TYPE
  T1             1             154
  T2             3             258
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  TMCO2 MUTATED     2   2     2
  TMCO2 WILD-TYPE 305  87    70
D114V5, multiclass
       clus
vv      TMCO2 MUTATED TMCO2 WILD-TYPE
  N0                2             305
  N1                2              87
  N2+N3             2              70
[1] 3 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
  TMCO2 MUTATED     3   0
  TMCO2 WILD-TYPE 324  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO2 MUTATED      3    0
  TMCO2 WILD-TYPE  324   23
   clus
vv  TMCO2 MUTATED TMCO2 WILD-TYPE
  0             3             324
  1             0              23
[1] 2 2
[1] FALSE
D114V7, binary
                 cls
clus                0   1
  TMCO2 MUTATED     3   3
  TMCO2 WILD-TYPE 256 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO2 MUTATED      3    3
  TMCO2 WILD-TYPE  256  218
        clus
vv       TMCO2 MUTATED TMCO2 WILD-TYPE
  FEMALE             3             256
  MALE               3             218
[1] 2 2
[1] FALSE
D114V8, continuous
[1] "Remove cluster labels:" "TMCO2 MUTATED"         
clus
  TMCO2 MUTATED TMCO2 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" "TMCO2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TMCO2 MUTATED                            0                                 2
  TMCO2 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TMCO2 MUTATED                                                    3
  TMCO2 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TMCO2 MUTATED                                            0
  TMCO2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TMCO2 MUTATED                                               0
  TMCO2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TMCO2 MUTATED                                0
  TMCO2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TMCO2 MUTATED                                    0
  TMCO2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TMCO2 MUTATED                              0                             0
  TMCO2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TMCO2 MUTATED                                               0
  TMCO2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TMCO2 MUTATED                              1
  TMCO2 WILD-TYPE                            8
D114V9, multiclass
                                                    clus
vv                                                   TMCO2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   TMCO2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V10, binary
                 cls
clus                0   1
  TMCO2 MUTATED     1   5
  TMCO2 WILD-TYPE  19 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO2 MUTATED      1    5
  TMCO2 WILD-TYPE   19  455
     clus
vv    TMCO2 MUTATED TMCO2 WILD-TYPE
  NO              1              19
  YES             5             455
[1] 2 2
[1] FALSE
D114V11, continuous
D114V12, continuous
                 vv
clus               R0  R1  R2  RX
  TMCO2 MUTATED     4   0   0   0
  TMCO2 WILD-TYPE 306  11   4  25
D114V13, multiclass
    clus
vv   TMCO2 MUTATED TMCO2 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMCO2 MUTATED                                  0     0
  TMCO2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMCO2 MUTATED                           2     4
  TMCO2 WILD-TYPE                        27   373
D114V14, multiclass
                                  clus
vv                                 TMCO2 MUTATED TMCO2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V15, binary
                 cls
clus                0   1
  TMCO2 MUTATED     0   5
  TMCO2 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO2 MUTATED      0    5
  TMCO2 WILD-TYPE    6  344
                        clus
vv                       TMCO2 MUTATED TMCO2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(115) Variable = N4BP1 MUTATION ANALYSIS
D115V1, survival
                 sevent
clus2               0   1
  N4BP1 MUTATED     7   0
  N4BP1 WILD-TYPE 308 141
  N4BP1 MUTATED N4BP1 WILD-TYPE 
              7             449 
  N4BP1 MUTATED N4BP1 WILD-TYPE 
              0             141 
$`N4BP1 MUTATED`
TCGA-50-5049 TCGA-55-8207 TCGA-55-8302 TCGA-86-8585 TCGA-97-8552 TCGA-MN-A4N4 
       70.55         2.17         0.76         1.15        20.58        38.63 
TCGA-NJ-A4YQ 
       29.13 

$`N4BP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.08         1.51        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       21.47        14.60        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64         0.26         0.43        19.82        59.11 

  N4BP1 MUTATED N4BP1 WILD-TYPE 
           0.76            0.00 
  N4BP1 MUTATED N4BP1 WILD-TYPE 
          70.55          223.96 
  N4BP1 MUTATED N4BP1 WILD-TYPE 
          20.58           17.98 
[1] "0.8 - 70.5 (20.6)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "9200000"
D115V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  N4BP1 MUTATED         1        3        4         0         0          1
  N4BP1 WILD-TYPE       3      120      129        46        67         69
                 vv
clus              STAGE IIIB STAGE IV
  N4BP1 MUTATED            0        0
  N4BP1 WILD-TYPE         11       25
D115V3, multiclass
            clus
vv           N4BP1 MUTATED N4BP1 WILD-TYPE
  STAGE I                1               3
  STAGE IA               3             120
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  N4BP1 MUTATED     3   5   1   0
  N4BP1 WILD-TYPE 152 256  42  18
D115V4, multiclass
    clus
vv   N4BP1 MUTATED N4BP1 WILD-TYPE
  T1             3             152
  T2             5             256
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  N4BP1 MUTATED     8   0     1
  N4BP1 WILD-TYPE 299  89    71
D115V5, multiclass
       clus
vv      N4BP1 MUTATED N4BP1 WILD-TYPE
  N0                8             299
  N1                0              89
  N2+N3             1              71
[1] 3 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
  N4BP1 MUTATED     6   0
  N4BP1 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP1 MUTATED      6    0
  N4BP1 WILD-TYPE  321   23
   clus
vv  N4BP1 MUTATED N4BP1 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D115V7, binary
                 cls
clus                0   1
  N4BP1 MUTATED     3   6
  N4BP1 WILD-TYPE 256 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP1 MUTATED      3    6
  N4BP1 WILD-TYPE  256  215
        clus
vv       N4BP1 MUTATED N4BP1 WILD-TYPE
  FEMALE             3             256
  MALE               6             215
[1] 2 2
[1] FALSE
D115V8, continuous
[1] "Remove cluster labels:" "N4BP1 MUTATED"         
clus
  N4BP1 MUTATED N4BP1 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
     TCGA-99-7458      TCGA-MN-A4N1      TCGA-MN-A4N5 
"N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" "N4BP1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  N4BP1 MUTATED                            1                                 1
  N4BP1 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  N4BP1 MUTATED                                                    4
  N4BP1 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  N4BP1 MUTATED                                            0
  N4BP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  N4BP1 MUTATED                                               1
  N4BP1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  N4BP1 MUTATED                                0
  N4BP1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  N4BP1 MUTATED                                    0
  N4BP1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  N4BP1 MUTATED                              0                             1
  N4BP1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  N4BP1 MUTATED                                               1
  N4BP1 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  N4BP1 MUTATED                              0
  N4BP1 WILD-TYPE                            9
D115V9, multiclass
                                                    clus
vv                                                   N4BP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   N4BP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V10, binary
                 cls
clus                0   1
  N4BP1 MUTATED     1   8
  N4BP1 WILD-TYPE  19 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP1 MUTATED      1    8
  N4BP1 WILD-TYPE   19  452
     clus
vv    N4BP1 MUTATED N4BP1 WILD-TYPE
  NO              1              19
  YES             8             452
[1] 2 2
[1] FALSE
D115V11, continuous
D115V12, continuous
                 vv
clus               R0  R1  R2  RX
  N4BP1 MUTATED     4   0   1   2
  N4BP1 WILD-TYPE 306  11   3  23
D115V13, multiclass
    clus
vv   N4BP1 MUTATED N4BP1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             1               3
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  N4BP1 MUTATED                                  0     0
  N4BP1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  N4BP1 MUTATED                           0     7
  N4BP1 WILD-TYPE                        29   370
D115V14, multiclass
                                  clus
vv                                 N4BP1 MUTATED N4BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V15, binary
                 cls
clus                0   1
  N4BP1 MUTATED     0   6
  N4BP1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP1 MUTATED      0    6
  N4BP1 WILD-TYPE    6  343
                        clus
vv                       N4BP1 MUTATED N4BP1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(116) Variable = MMP13 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2               0   1
  MMP13 MUTATED    10   3
  MMP13 WILD-TYPE 305 138
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             443 
  MMP13 MUTATED MMP13 WILD-TYPE 
              3             138 
$`MMP13 MUTATED`
TCGA-05-4250 TCGA-05-4424 TCGA-35-4123 TCGA-44-6777 TCGA-44-8117 TCGA-44-A47A 
        3.98        30.02         5.98        32.45        12.66        15.32 
TCGA-49-6767 TCGA-55-8506 TCGA-64-5774 TCGA-86-8674 TCGA-91-6831 TCGA-95-7567 
       22.26         0.36        87.98        13.32        10.19        18.67 
TCGA-MP-A4TE 
       29.46 

$`MMP13 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       17.59        23.64         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       29.26        17.16        11.64        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
       29.92        56.81        20.65        55.43        38.37         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        14.96        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36         1.97         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23         2.43        10.09        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  MMP13 MUTATED MMP13 WILD-TYPE 
           0.36            0.00 
  MMP13 MUTATED MMP13 WILD-TYPE 
          87.98          223.96 
  MMP13 MUTATED MMP13 WILD-TYPE 
          15.32           18.08 
[1] "0.4 - 88.0 (15.3)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D116V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MMP13 MUTATED         0        1        5         2         4          1
  MMP13 WILD-TYPE       4      122      128        44        63         69
                 vv
clus              STAGE IIIB STAGE IV
  MMP13 MUTATED            0        0
  MMP13 WILD-TYPE         11       25
D116V3, multiclass
            clus
vv           MMP13 MUTATED MMP13 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               5             128
  STAGE IIA              2              44
  STAGE IIB              4              63
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP13 MUTATED     1   8   4   0
  MMP13 WILD-TYPE 154 253  39  18
D116V4, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  T1             1             154
  T2             8             253
  T3             4              39
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  MMP13 MUTATED     9   3     0
  MMP13 WILD-TYPE 298  86    72
D116V5, multiclass
       clus
vv      MMP13 MUTATED MMP13 WILD-TYPE
  N0                9             298
  N1                3              86
  N2+N3             0              72
[1] 3 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
  MMP13 MUTATED     7   0
  MMP13 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      7    0
  MMP13 WILD-TYPE  320   23
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D116V7, binary
                 cls
clus                0   1
  MMP13 MUTATED     6   7
  MMP13 WILD-TYPE 253 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      6    7
  MMP13 WILD-TYPE  253  214
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE             6             253
  MALE               7             214
[1] 2 2
[1] FALSE
D116V8, continuous
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-5375      TCGA-53-A4EZ      TCGA-55-7283 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MMP13 MUTATED                            0                                 2
  MMP13 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MMP13 MUTATED                                                   10
  MMP13 WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MMP13 MUTATED                                            0
  MMP13 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MMP13 MUTATED                                               0
  MMP13 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MMP13 MUTATED                                0
  MMP13 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MMP13 MUTATED                                    0
  MMP13 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MMP13 MUTATED                              0                             1
  MMP13 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MMP13 MUTATED                                               0
  MMP13 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MMP13 MUTATED                              0
  MMP13 WILD-TYPE                            9
D116V9, multiclass
                                                    clus
vv                                                   MMP13 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MMP13 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V10, binary
                 cls
clus                0   1
  MMP13 MUTATED     1  12
  MMP13 WILD-TYPE  19 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      1   12
  MMP13 WILD-TYPE   19  448
     clus
vv    MMP13 MUTATED MMP13 WILD-TYPE
  NO              1              19
  YES            12             448
[1] 2 2
[1] FALSE
D116V11, continuous
D116V12, continuous
                 vv
clus               R0  R1  R2  RX
  MMP13 MUTATED     6   1   1   1
  MMP13 WILD-TYPE 304  10   3  24
D116V13, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  R0             6             304
  R1             1              10
  R2             1               3
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP13 MUTATED                                  0     0
  MMP13 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED                           0    11
  MMP13 WILD-TYPE                        29   366
D116V14, multiclass
                                  clus
vv                                 MMP13 MUTATED MMP13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V15, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   9
  MMP13 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    9
  MMP13 WILD-TYPE    6  340
                        clus
vv                       MMP13 MUTATED MMP13 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(117) Variable = ZACN MUTATION ANALYSIS
D117V1, survival
                sevent
clus2              0   1
  ZACN MUTATED     7   1
  ZACN WILD-TYPE 308 140
  ZACN MUTATED ZACN WILD-TYPE 
             8            448 
  ZACN MUTATED ZACN WILD-TYPE 
             1            140 
$`ZACN MUTATED`
TCGA-44-8119 TCGA-50-5049 TCGA-55-8506 TCGA-55-8511 TCGA-86-A456 TCGA-97-A4M3 
        3.25        70.55         0.36         0.30        13.32        17.75 
TCGA-J2-A4AG TCGA-MP-A4TK 
       16.44        19.13 

$`ZACN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       17.16        11.64        22.26        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       20.52        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       35.47        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ZACN MUTATED ZACN WILD-TYPE 
           0.3            0.0 
  ZACN MUTATED ZACN WILD-TYPE 
         70.55         223.96 
  ZACN MUTATED ZACN WILD-TYPE 
         14.88          18.15 
[1] "0.3 - 70.5 (14.9)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.8"
D117V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZACN MUTATED         0        4        1         0         3          0
  ZACN WILD-TYPE       4      119      132        46        64         70
                vv
clus             STAGE IIIB STAGE IV
  ZACN MUTATED            0        0
  ZACN WILD-TYPE         11       25
D117V3, multiclass
            clus
vv           ZACN MUTATED ZACN WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              1            132
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZACN MUTATED     3   3   2   0
  ZACN WILD-TYPE 152 258  41  18
D117V4, multiclass
    clus
vv   ZACN MUTATED ZACN WILD-TYPE
  T1            3            152
  T2            3            258
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  ZACN MUTATED     7   1     0
  ZACN WILD-TYPE 300  88    72
D117V5, multiclass
       clus
vv      ZACN MUTATED ZACN WILD-TYPE
  N0               7            300
  N1               1             88
  N2+N3            0             72
[1] 3 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
  ZACN MUTATED     4   0
  ZACN WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      4    0
  ZACN WILD-TYPE  323   23
   clus
vv  ZACN MUTATED ZACN WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D117V7, binary
                cls
clus               0   1
  ZACN MUTATED     6   2
  ZACN WILD-TYPE 253 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      6    2
  ZACN WILD-TYPE  253  219
        clus
vv       ZACN MUTATED ZACN WILD-TYPE
  FEMALE            6            253
  MALE              2            219
[1] 2 2
[1] FALSE
D117V8, continuous
[1] "Remove cluster labels:" "ZACN MUTATED"          
clus
  ZACN MUTATED ZACN WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8512 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZACN MUTATED                            0                                 1
  ZACN WILD-TYPE                         18                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZACN MUTATED                                                    6
  ZACN WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZACN MUTATED                                            0
  ZACN WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZACN MUTATED                                               0
  ZACN WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  ZACN MUTATED                                0
  ZACN WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  ZACN MUTATED                                    0
  ZACN WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZACN MUTATED                              0                             1
  ZACN WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZACN MUTATED                                               0
  ZACN WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  ZACN MUTATED                              0
  ZACN WILD-TYPE                            9
D117V9, multiclass
                                                    clus
vv                                                   ZACN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   ZACN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V10, binary
                cls
clus               0   1
  ZACN MUTATED     1   7
  ZACN WILD-TYPE  19 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      1    7
  ZACN WILD-TYPE   19  453
     clus
vv    ZACN MUTATED ZACN WILD-TYPE
  NO             1             19
  YES            7            453
[1] 2 2
[1] FALSE
D117V11, continuous
D117V12, continuous
                vv
clus              R0  R1  R2  RX
  ZACN MUTATED     5   0   0   0
  ZACN WILD-TYPE 305  11   4  25
D117V13, multiclass
    clus
vv   ZACN MUTATED ZACN WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZACN MUTATED                                  0     1
  ZACN WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZACN MUTATED                           0     6
  ZACN WILD-TYPE                        29   371
D117V14, multiclass
                                  clus
vv                                 ZACN MUTATED ZACN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       6            371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V15, binary
                cls
clus               0   1
  ZACN MUTATED     0   7
  ZACN WILD-TYPE   6 342
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      0    7
  ZACN WILD-TYPE    6  342
                        clus
vv                       ZACN MUTATED ZACN WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            7            342
[1] 2 2
[1] FALSE

Clustering(118) Variable = SFTPB MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2               0   1
  SFTPB MUTATED     4   2
  SFTPB WILD-TYPE 311 139
  SFTPB MUTATED SFTPB WILD-TYPE 
              6             450 
  SFTPB MUTATED SFTPB WILD-TYPE 
              2             139 
$`SFTPB MUTATED`
TCGA-38-4631 TCGA-55-6968 TCGA-55-8207 TCGA-55-8616 TCGA-86-6851 TCGA-MN-A4N1 
       11.64        42.51         2.17         1.58         5.88        27.19 

$`SFTPB WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65         0.79        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SFTPB MUTATED SFTPB WILD-TYPE 
           1.58            0.00 
  SFTPB MUTATED SFTPB WILD-TYPE 
          42.51          223.96 
  SFTPB MUTATED SFTPB WILD-TYPE 
           8.76           18.10 
[1] "1.6 - 42.5 (8.8)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D118V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SFTPB MUTATED         0        0        3         2         0          0
  SFTPB WILD-TYPE       4      123      130        44        67         70
                 vv
clus              STAGE IIIB STAGE IV
  SFTPB MUTATED            0        1
  SFTPB WILD-TYPE         11       24
D118V3, multiclass
            clus
vv           SFTPB MUTATED SFTPB WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               3             130
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SFTPB MUTATED     2   4   0   0
  SFTPB WILD-TYPE 153 257  43  18
D118V4, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  T1             2             153
  T2             4             257
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  SFTPB MUTATED     4   2     0
  SFTPB WILD-TYPE 303  87    72
D118V5, multiclass
       clus
vv      SFTPB MUTATED SFTPB WILD-TYPE
  N0                4             303
  N1                2              87
  N2+N3             0              72
[1] 3 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
  SFTPB MUTATED     4   1
  SFTPB WILD-TYPE 323  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      4    1
  SFTPB WILD-TYPE  323   22
   clus
vv  SFTPB MUTATED SFTPB WILD-TYPE
  0             4             323
  1             1              22
[1] 2 2
[1] FALSE
D118V7, binary
                 cls
clus                0   1
  SFTPB MUTATED     3   3
  SFTPB WILD-TYPE 256 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      3    3
  SFTPB WILD-TYPE  256  218
        clus
vv       SFTPB MUTATED SFTPB WILD-TYPE
  FEMALE             3             256
  MALE               3             218
[1] 2 2
[1] FALSE
D118V8, continuous
[1] "Remove cluster labels:" "SFTPB MUTATED"         
clus
  SFTPB MUTATED SFTPB WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-99-7458      TCGA-MN-A4N4      TCGA-MN-A4N5 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SFTPB MUTATED                            1                                 1
  SFTPB WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SFTPB MUTATED                                                    4
  SFTPB WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SFTPB MUTATED                                            0
  SFTPB WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SFTPB MUTATED                                               0
  SFTPB WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SFTPB MUTATED                                0
  SFTPB WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SFTPB MUTATED                                    0
  SFTPB WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SFTPB MUTATED                              0                             0
  SFTPB WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SFTPB MUTATED                                               0
  SFTPB WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SFTPB MUTATED                              0
  SFTPB WILD-TYPE                            9
D118V9, multiclass
                                                    clus
vv                                                   SFTPB MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SFTPB WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V10, binary
                 cls
clus                0   1
  SFTPB MUTATED     0   6
  SFTPB WILD-TYPE  20 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      0    6
  SFTPB WILD-TYPE   20  454
     clus
vv    SFTPB MUTATED SFTPB WILD-TYPE
  NO              0              20
  YES             6             454
[1] 2 2
[1] FALSE
D118V11, continuous
[1] "Remove cluster labels:" "SFTPB MUTATED"         
clus
  SFTPB MUTATED SFTPB WILD-TYPE 
              2             331 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4396 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4397      TCGA-05-4398      TCGA-05-4405      TCGA-05-4410 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4415      TCGA-05-4417      TCGA-05-4418      TCGA-05-4420 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4422      TCGA-05-4424      TCGA-05-4425      TCGA-05-4426 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4430      TCGA-05-4432      TCGA-05-4433 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4434      TCGA-05-5420      TCGA-05-5423      TCGA-05-5425 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-5428      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-38-4625      TCGA-38-4626      TCGA-38-4629      TCGA-38-4632 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3398      TCGA-44-3918      TCGA-44-4112 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-5643      TCGA-44-5644      TCGA-44-5645      TCGA-44-6144 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-6145      TCGA-44-6146      TCGA-44-6148      TCGA-44-6774 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-6775      TCGA-44-6776      TCGA-44-6777      TCGA-44-6778 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-6779      TCGA-44-7659      TCGA-44-7660      TCGA-44-7661 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-7662      TCGA-44-7667      TCGA-44-7669      TCGA-44-7670 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-7672      TCGA-44-8117      TCGA-44-8119      TCGA-44-8120 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47F 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU      TCGA-49-4486 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-49-4487      TCGA-49-4490      TCGA-49-4494      TCGA-49-4505 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-49-4506      TCGA-49-4507      TCGA-49-4510      TCGA-49-4514 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-49-6745 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-49-6761      TCGA-49-6767      TCGA-50-5051      TCGA-50-5072 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-50-5931      TCGA-50-5939      TCGA-50-5941      TCGA-50-5942 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-50-6590      TCGA-50-7109      TCGA-50-8457      TCGA-50-8459 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-6543      TCGA-55-6971      TCGA-55-6983      TCGA-55-6985 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7281      TCGA-55-7283      TCGA-55-7574      TCGA-55-7724 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7903 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7907      TCGA-55-7910      TCGA-55-7911      TCGA-55-7914 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7994      TCGA-55-7995      TCGA-55-8089      TCGA-55-8092 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8094      TCGA-55-8096      TCGA-55-8097      TCGA-55-8203 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8208      TCGA-55-8299      TCGA-55-8301 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8302      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8614      TCGA-55-8615      TCGA-55-8620 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A491      TCGA-55-A492      TCGA-55-A493 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG      TCGA-62-8398 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-62-8399      TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-62-A46S      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-64-1676      TCGA-64-1677      TCGA-64-1679      TCGA-64-5774 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-64-5815      TCGA-69-7761      TCGA-69-7763      TCGA-69-7764 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-69-7973      TCGA-69-7974      TCGA-69-7978      TCGA-69-7979 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-69-7980      TCGA-69-8253      TCGA-69-8254      TCGA-69-8255 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4658      TCGA-73-4659      TCGA-73-4662 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4668      TCGA-73-4670      TCGA-73-4675 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-75-5122      TCGA-75-5125 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-75-5126      TCGA-75-6203      TCGA-75-6206      TCGA-75-6207 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-75-6211      TCGA-75-6214      TCGA-75-7027      TCGA-75-7031 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-80-5608      TCGA-80-5611      TCGA-83-5908      TCGA-86-7701 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7714      TCGA-86-7954      TCGA-86-8054 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8358      TCGA-86-8359      TCGA-86-8669 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8673      TCGA-86-8674      TCGA-91-6829      TCGA-91-6830 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-91-6835      TCGA-91-6836      TCGA-91-6840      TCGA-91-6849 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-91-7771      TCGA-91-8499      TCGA-91-A4BC      TCGA-93-7347 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-95-7039      TCGA-95-7043      TCGA-95-7562      TCGA-95-7944 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-95-7947      TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547      TCGA-97-7552 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7937      TCGA-97-7938 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-7941      TCGA-97-8171      TCGA-97-8172      TCGA-97-8174 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-8176      TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-A4M1      TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025      TCGA-99-8028 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-99-8032      TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-L4-A4E5      TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY      TCGA-MP-A4T2 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7      TCGA-MP-A4T8 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TD 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YF      TCGA-NJ-A4YG 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ      TCGA-NJ-A55A 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
D118V12, continuous
[1] "Remove cluster labels:" "SFTPB MUTATED"         
clus
  SFTPB MUTATED SFTPB WILD-TYPE 
              2             255 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6642 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-6712      TCGA-55-6971      TCGA-55-7227      TCGA-55-7283 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7907 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-8089 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8506      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8615      TCGA-55-8620      TCGA-55-8621 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-55-A491      TCGA-55-A492      TCGA-55-A493      TCGA-55-A494 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-62-8398      TCGA-64-1677      TCGA-64-1681      TCGA-64-5774 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-69-7761      TCGA-69-7763      TCGA-69-7764      TCGA-69-7765 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7979      TCGA-69-8253      TCGA-69-8255 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4675      TCGA-73-4676 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-73-7498      TCGA-75-6214      TCGA-75-7025      TCGA-75-7027 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7145      TCGA-78-7146      TCGA-78-7147 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7148      TCGA-78-7149      TCGA-78-7150      TCGA-78-7152 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7153      TCGA-78-7154      TCGA-78-7155      TCGA-78-7156 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7158      TCGA-78-7159      TCGA-78-7160      TCGA-78-7161 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7162      TCGA-78-7163      TCGA-78-7166      TCGA-78-7167 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7220      TCGA-78-7535      TCGA-78-7536      TCGA-78-7537 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-7539      TCGA-78-7542      TCGA-78-7633      TCGA-78-8640 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-78-8648      TCGA-78-8655      TCGA-78-8660      TCGA-78-8662 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-80-5607      TCGA-80-5608      TCGA-83-5908      TCGA-86-7711 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-8054      TCGA-86-8055 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8281 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8673 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-91-6829      TCGA-91-6830 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-91-6836      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7567      TCGA-95-7944      TCGA-95-7947 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8176 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N4 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4T2 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8      TCGA-MP-A4T9 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE      TCGA-MP-A4TF 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"SFTPB WILD-TYPE" "SFTPB WILD-TYPE" "SFTPB WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  SFTPB MUTATED     4   0   0   0
  SFTPB WILD-TYPE 306  11   4  25
D118V13, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFTPB MUTATED                                  0     0
  SFTPB WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SFTPB MUTATED                           1     5
  SFTPB WILD-TYPE                        28   372
D118V14, multiclass
                                  clus
vv                                 SFTPB MUTATED SFTPB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V15, binary
                 cls
clus                0   1
  SFTPB MUTATED     0   6
  SFTPB WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      0    6
  SFTPB WILD-TYPE    6  343
                        clus
vv                       SFTPB MUTATED SFTPB WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(119) Variable = SRRM3 MUTATION ANALYSIS
D119V1, survival
                 sevent
clus2               0   1
  SRRM3 MUTATED     3   1
  SRRM3 WILD-TYPE 312 140
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              4             452 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              1             140 
$`SRRM3 MUTATED`
TCGA-50-6590 TCGA-69-7760 TCGA-86-8073 TCGA-99-8032 
       42.35         6.64        24.33         1.45 

$`SRRM3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       15.12        18.64        29.03        25.12        22.55         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        34.85        36.76         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SRRM3 MUTATED SRRM3 WILD-TYPE 
           1.45            0.00 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
          42.35          223.96 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
         15.485          18.030 
[1] "1.4 - 42.4 (15.5)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1"  
D119V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SRRM3 MUTATED         0        1        3         0         1          0
  SRRM3 WILD-TYPE       4      122      130        46        66         70
                 vv
clus              STAGE IIIB STAGE IV
  SRRM3 MUTATED            0        0
  SRRM3 WILD-TYPE         11       25
D119V3, multiclass
            clus
vv           SRRM3 MUTATED SRRM3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SRRM3 MUTATED     1   2   2   0
  SRRM3 WILD-TYPE 154 259  41  18
D119V4, multiclass
    clus
vv   SRRM3 MUTATED SRRM3 WILD-TYPE
  T1             1             154
  T2             2             259
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  SRRM3 MUTATED     5   0     0
  SRRM3 WILD-TYPE 302  89    72
D119V5, multiclass
       clus
vv      SRRM3 MUTATED SRRM3 WILD-TYPE
  N0                5             302
  N1                0              89
  N2+N3             0              72
[1] 3 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
  SRRM3 MUTATED     5   0
  SRRM3 WILD-TYPE 322  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      5    0
  SRRM3 WILD-TYPE  322   23
   clus
vv  SRRM3 MUTATED SRRM3 WILD-TYPE
  0             5             322
  1             0              23
[1] 2 2
[1] FALSE
D119V7, binary
                 cls
clus                0   1
  SRRM3 MUTATED     1   4
  SRRM3 WILD-TYPE 258 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      1    4
  SRRM3 WILD-TYPE  258  217
        clus
vv       SRRM3 MUTATED SRRM3 WILD-TYPE
  FEMALE             1             258
  MALE               4             217
[1] 2 2
[1] FALSE
D119V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SRRM3 MUTATED                            1                                 0
  SRRM3 WILD-TYPE                         17                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SRRM3 MUTATED                                                    3
  SRRM3 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SRRM3 MUTATED                                            0
  SRRM3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SRRM3 MUTATED                                               1
  SRRM3 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SRRM3 MUTATED                                0
  SRRM3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SRRM3 MUTATED                                    0
  SRRM3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SRRM3 MUTATED                              0                             0
  SRRM3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SRRM3 MUTATED                                               0
  SRRM3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SRRM3 MUTATED                              0
  SRRM3 WILD-TYPE                            9
D119V9, multiclass
                                                    clus
vv                                                   SRRM3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SRRM3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V10, binary
                 cls
clus                0   1
  SRRM3 MUTATED     0   5
  SRRM3 WILD-TYPE  20 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      0    5
  SRRM3 WILD-TYPE   20  455
     clus
vv    SRRM3 MUTATED SRRM3 WILD-TYPE
  NO              0              20
  YES             5             455
[1] 2 2
[1] FALSE
D119V11, continuous
D119V12, continuous
[1] "Remove cluster labels:" "SRRM3 MUTATED"         
clus
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              2             255 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6642 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-6712      TCGA-55-6971      TCGA-55-7227      TCGA-55-7283 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7907 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-8089 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-8506      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8615      TCGA-55-8620      TCGA-55-8621 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-55-A491      TCGA-55-A492      TCGA-55-A493      TCGA-55-A494 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-62-8398      TCGA-64-1677      TCGA-64-1681      TCGA-64-5774 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-69-7761      TCGA-69-7763      TCGA-69-7764      TCGA-69-7765 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7979      TCGA-69-8253      TCGA-69-8255 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4675      TCGA-73-4676 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-73-7498      TCGA-75-6214      TCGA-75-7025      TCGA-75-7027 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7145      TCGA-78-7146      TCGA-78-7147 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-78-7148      TCGA-78-7149      TCGA-78-7150      TCGA-78-7152 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-78-7153      TCGA-78-7154      TCGA-78-7155      TCGA-78-7156 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-78-7158      TCGA-78-7159      TCGA-78-7160      TCGA-78-7161 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-78-7162      TCGA-78-7163      TCGA-78-7166      TCGA-78-7167 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-78-7220      TCGA-78-7535      TCGA-78-7536      TCGA-78-7537 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-78-7539      TCGA-78-7542      TCGA-78-7633      TCGA-78-8640 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-78-8648      TCGA-78-8655      TCGA-78-8660      TCGA-78-8662 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-80-5607      TCGA-80-5608      TCGA-83-5908      TCGA-86-6851 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7714      TCGA-86-7954      TCGA-86-8054 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8281 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8673 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-91-6829      TCGA-91-6830 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7567      TCGA-95-7944      TCGA-95-7947 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8176 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-J2-8194 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4T2 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8      TCGA-MP-A4T9 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE      TCGA-MP-A4TF 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  SRRM3 MUTATED     3   0   0   0
  SRRM3 WILD-TYPE 307  11   4  25
D119V13, multiclass
    clus
vv   SRRM3 MUTATED SRRM3 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRRM3 MUTATED                                  0     0
  SRRM3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SRRM3 MUTATED                           0     5
  SRRM3 WILD-TYPE                        29   372
D119V14, multiclass
                                  clus
vv                                 SRRM3 MUTATED SRRM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V15, binary
                 cls
clus                0   1
  SRRM3 MUTATED     0   5
  SRRM3 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      0    5
  SRRM3 WILD-TYPE    6  344
                        clus
vv                       SRRM3 MUTATED SRRM3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(120) Variable = FAM71A MUTATION ANALYSIS
D120V1, survival
                  sevent
clus2                0   1
  FAM71A MUTATED    10   5
  FAM71A WILD-TYPE 305 136
  FAM71A MUTATED FAM71A WILD-TYPE 
              15              441 
  FAM71A MUTATED FAM71A WILD-TYPE 
               5              136 
$`FAM71A MUTATED`
TCGA-05-4397 TCGA-44-6145 TCGA-55-1592 TCGA-55-6975 TCGA-55-6982 TCGA-55-8089 
       24.03        10.78        23.05         3.88        32.71         3.29 
TCGA-55-8506 TCGA-67-3771 TCGA-86-8054 TCGA-86-8073 TCGA-91-6847 TCGA-95-7039 
        0.36        20.05        24.49        24.33        27.68         1.12 
TCGA-MN-A4N4 TCGA-MP-A4T7 TCGA-NJ-A55R 
       38.63         5.49        19.82 

$`FAM71A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 
       33.30        28.37        12.59        23.77         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 
       42.51        40.73        15.25         0.82        48.49         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.43        19.89        16.70         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       86.04        58.85         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.26         0.43        59.11 

  FAM71A MUTATED FAM71A WILD-TYPE 
            0.36             0.00 
  FAM71A MUTATED FAM71A WILD-TYPE 
           38.63           223.96 
  FAM71A MUTATED FAM71A WILD-TYPE 
           20.05            17.92 
[1] "0.4 - 38.6 (20.1)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.6"
D120V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FAM71A MUTATED         0        6        2         0         6          0
  FAM71A WILD-TYPE       4      117      131        46        61         70
                  vv
clus               STAGE IIIB STAGE IV
  FAM71A MUTATED            0        1
  FAM71A WILD-TYPE         11       24
D120V3, multiclass
            clus
vv           FAM71A MUTATED FAM71A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                6              117
  STAGE IB                2              131
  STAGE IIA               0               46
  STAGE IIB               6               61
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM71A MUTATED     5   8   2   0
  FAM71A WILD-TYPE 150 253  41  18
D120V4, multiclass
    clus
vv   FAM71A MUTATED FAM71A WILD-TYPE
  T1              5              150
  T2              8              253
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  FAM71A MUTATED    11   4     0
  FAM71A WILD-TYPE 296  85    72
D120V5, multiclass
       clus
vv      FAM71A MUTATED FAM71A WILD-TYPE
  N0                11              296
  N1                 4               85
  N2+N3              0               72
[1] 3 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
  FAM71A MUTATED    10   1
  FAM71A WILD-TYPE 317  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM71A MUTATED     10    1
  FAM71A WILD-TYPE  317   22
   clus
vv  FAM71A MUTATED FAM71A WILD-TYPE
  0             10              317
  1              1               22
[1] 2 2
[1] FALSE
D120V7, binary
                  cls
clus                 0   1
  FAM71A MUTATED     7   8
  FAM71A WILD-TYPE 252 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM71A MUTATED      7    8
  FAM71A WILD-TYPE  252  213
        clus
vv       FAM71A MUTATED FAM71A WILD-TYPE
  FEMALE              7              252
  MALE                8              213
[1] 2 2
[1] FALSE
D120V8, continuous
[1] "Remove cluster labels:" "FAM71A MUTATED"        
clus
  FAM71A MUTATED FAM71A WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8096       TCGA-55-8205       TCGA-55-8208 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N5 
"FAM71A WILD-TYPE" "FAM71A WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FAM71A MUTATED                            1                                 3
  FAM71A WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FAM71A MUTATED                                                   10
  FAM71A WILD-TYPE                                                284
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FAM71A MUTATED                                            0
  FAM71A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FAM71A MUTATED                                               1
  FAM71A WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  FAM71A MUTATED                                0
  FAM71A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  FAM71A MUTATED                                    0
  FAM71A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FAM71A MUTATED                              0                             0
  FAM71A WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FAM71A MUTATED                                               0
  FAM71A WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  FAM71A MUTATED                              0
  FAM71A WILD-TYPE                            9
D120V9, multiclass
                                                    clus
vv                                                   FAM71A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   FAM71A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V10, binary
                  cls
clus                 0   1
  FAM71A MUTATED     0  15
  FAM71A WILD-TYPE  20 445
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM71A MUTATED      0   15
  FAM71A WILD-TYPE   20  445
     clus
vv    FAM71A MUTATED FAM71A WILD-TYPE
  NO               0               20
  YES             15              445
[1] 2 2
[1] FALSE
D120V11, continuous
D120V12, continuous
                  vv
clus                R0  R1  R2  RX
  FAM71A MUTATED     9   0   0   0
  FAM71A WILD-TYPE 301  11   4  25
D120V13, multiclass
    clus
vv   FAM71A MUTATED FAM71A WILD-TYPE
  R0              9              301
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM71A MUTATED                                  0     0
  FAM71A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM71A MUTATED                           1    12
  FAM71A WILD-TYPE                        28   365
D120V14, multiclass
                                  clus
vv                                 FAM71A MUTATED FAM71A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        12              365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V15, binary
                  cls
clus                 0   1
  FAM71A MUTATED     0  12
  FAM71A WILD-TYPE   6 337
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM71A MUTATED      0   12
  FAM71A WILD-TYPE    6  337
                        clus
vv                       FAM71A MUTATED FAM71A WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             12              337
[1] 2 2
[1] FALSE

Clustering(121) Variable = MCM9 MUTATION ANALYSIS
D121V1, survival
                sevent
clus2              0   1
  MCM9 MUTATED     2   1
  MCM9 WILD-TYPE 313 140
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            453 
  MCM9 MUTATED MCM9 WILD-TYPE 
             1            140 
$`MCM9 MUTATED`
TCGA-38-4625 TCGA-49-4486 TCGA-69-7979 
       97.74        76.21         2.93 

$`MCM9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MCM9 MUTATED MCM9 WILD-TYPE 
          2.93           0.00 
  MCM9 MUTATED MCM9 WILD-TYPE 
         97.74         223.96 
  MCM9 MUTATED MCM9 WILD-TYPE 
         76.21          17.98 
[1] "2.9 - 97.7 (76.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.8"
D121V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MCM9 MUTATED         0        1        2         0         0          0
  MCM9 WILD-TYPE       4      122      131        46        67         70
                vv
clus             STAGE IIIB STAGE IV
  MCM9 MUTATED            0        0
  MCM9 WILD-TYPE         11       25
D121V3, multiclass
            clus
vv           MCM9 MUTATED MCM9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            131
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCM9 MUTATED     1   2   0   0
  MCM9 WILD-TYPE 154 259  43  18
D121V4, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  T1            1            154
  T2            2            259
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  MCM9 MUTATED     3   0     0
  MCM9 WILD-TYPE 304  89    72
D121V5, multiclass
       clus
vv      MCM9 MUTATED MCM9 WILD-TYPE
  N0               3            304
  N1               0             89
  N2+N3            0             72
[1] 3 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
  MCM9 MUTATED     2   0
  MCM9 WILD-TYPE 325  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      2    0
  MCM9 WILD-TYPE  325   23
   clus
vv  MCM9 MUTATED MCM9 WILD-TYPE
  0            2            325
  1            0             23
[1] 2 2
[1] FALSE
D121V7, binary
                cls
clus               0   1
  MCM9 MUTATED     2   1
  MCM9 WILD-TYPE 257 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      2    1
  MCM9 WILD-TYPE  257  220
        clus
vv       MCM9 MUTATED MCM9 WILD-TYPE
  FEMALE            2            257
  MALE              1            220
[1] 2 2
[1] FALSE
D121V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MCM9 MUTATED                            1                                 0
  MCM9 WILD-TYPE                         17                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MCM9 MUTATED                                                    2
  MCM9 WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MCM9 MUTATED                                            0
  MCM9 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MCM9 MUTATED                                               0
  MCM9 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MCM9 MUTATED                                0
  MCM9 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MCM9 MUTATED                                    0
  MCM9 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MCM9 MUTATED                              0                             0
  MCM9 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MCM9 MUTATED                                               0
  MCM9 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MCM9 MUTATED                              0
  MCM9 WILD-TYPE                            9
D121V9, multiclass
                                                    clus
vv                                                   MCM9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MCM9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V10, binary
                cls
clus               0   1
  MCM9 MUTATED     0   3
  MCM9 WILD-TYPE  20 457
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      0    3
  MCM9 WILD-TYPE   20  457
     clus
vv    MCM9 MUTATED MCM9 WILD-TYPE
  NO             0             20
  YES            3            457
[1] 2 2
[1] FALSE
D121V11, continuous
D121V12, continuous
                vv
clus              R0  R1  R2  RX
  MCM9 MUTATED     2   0   0   0
  MCM9 WILD-TYPE 308  11   4  25
D121V13, multiclass
[1] "Remove cluster labels:" "MCM9 MUTATED"          
clus
  MCM9 MUTATED MCM9 WILD-TYPE 
             2            348 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-4123 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4626     TCGA-38-4627     TCGA-38-4628 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-38-4629     TCGA-38-4630     TCGA-38-4631     TCGA-38-4632 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F     TCGA-44-2657 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-2661     TCGA-44-2665     TCGA-44-3396     TCGA-44-3398 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-3919     TCGA-44-4112     TCGA-44-6144 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4487 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4488     TCGA-49-4494     TCGA-49-4501     TCGA-49-4505 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4507     TCGA-49-4510     TCGA-49-4512 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4514     TCGA-49-6742     TCGA-49-6744     TCGA-49-6761 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-6767     TCGA-50-5051     TCGA-50-5055     TCGA-50-5066 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-50-6597     TCGA-50-6673     TCGA-50-8460     TCGA-53-7624 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-1592     TCGA-55-5899 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6970     TCGA-55-6971     TCGA-55-6972 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-6980     TCGA-55-6981     TCGA-55-6983     TCGA-55-6985 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7281     TCGA-55-7284     TCGA-55-7570     TCGA-55-7574 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7576     TCGA-55-7724     TCGA-55-7725     TCGA-55-7726 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7727     TCGA-55-7728     TCGA-55-7815     TCGA-55-7903 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8085     TCGA-55-8087 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8090     TCGA-55-8091     TCGA-55-8092 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8203     TCGA-55-8204 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8206     TCGA-55-8207     TCGA-55-8208 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8505 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8508     TCGA-55-8510 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8513     TCGA-55-8514 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8614     TCGA-55-8615     TCGA-55-8616     TCGA-55-8619 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-1676     TCGA-64-1677     TCGA-64-1679     TCGA-64-1681 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-5781     TCGA-64-5815     TCGA-67-3771     TCGA-67-3773 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-67-4679     TCGA-67-6215     TCGA-67-6216     TCGA-67-6217 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4658     TCGA-73-4659 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-7499     TCGA-75-5122     TCGA-75-5125     TCGA-75-5126 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-5146     TCGA-75-5147     TCGA-75-6203     TCGA-75-6205 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-6206     TCGA-75-6207     TCGA-75-6211     TCGA-75-6212 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7030 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7143     TCGA-78-7145     TCGA-78-7146 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7147     TCGA-78-7148     TCGA-78-7149     TCGA-78-7150 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7152     TCGA-78-7153     TCGA-78-7154     TCGA-78-7155 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7156     TCGA-78-7158     TCGA-78-7159     TCGA-78-7160 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7166 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7167     TCGA-78-7220     TCGA-78-7535     TCGA-78-7536 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7537     TCGA-78-7539     TCGA-78-7540     TCGA-78-7542 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-80-5611     TCGA-83-5908     TCGA-86-6562     TCGA-86-7701 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-7711     TCGA-86-7713     TCGA-86-7714     TCGA-86-7953 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8054     TCGA-86-8055 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8585     TCGA-86-8668 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-8672     TCGA-86-8673 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-91-6828     TCGA-91-6829     TCGA-91-6835     TCGA-91-6840 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-7546 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-97-7554     TCGA-97-7938     TCGA-97-7941     TCGA-97-8176 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-99-8028     TCGA-99-8032     TCGA-99-8033     TCGA-J2-A4AD 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCM9 MUTATED                                  0     0
  MCM9 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCM9 MUTATED                           0     3
  MCM9 WILD-TYPE                        29   374
D121V14, multiclass
                                  clus
vv                                 MCM9 MUTATED MCM9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       3            374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V15, binary
                cls
clus               0   1
  MCM9 MUTATED     0   3
  MCM9 WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      0    3
  MCM9 WILD-TYPE    6  346
                        clus
vv                       MCM9 MUTATED MCM9 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(122) Variable = GRAP2 MUTATION ANALYSIS
D122V1, survival
                 sevent
clus2               0   1
  GRAP2 MUTATED     8   2
  GRAP2 WILD-TYPE 307 139
  GRAP2 MUTATED GRAP2 WILD-TYPE 
             10             446 
  GRAP2 MUTATED GRAP2 WILD-TYPE 
              2             139 
$`GRAP2 MUTATED`
TCGA-44-6145 TCGA-44-8120 TCGA-50-5049 TCGA-50-5930 TCGA-55-6972 TCGA-55-8507 
       10.78         8.55        70.55         9.27        48.49         0.26 
TCGA-55-8620 TCGA-55-A4DF TCGA-86-8073 TCGA-97-8179 
        2.17        20.19        24.33        14.30 

$`GRAP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 
       26.56        33.30        28.37        12.59        23.77         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.36         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
        6.64        17.62         0.49         1.58         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  GRAP2 MUTATED GRAP2 WILD-TYPE 
           0.26            0.00 
  GRAP2 MUTATED GRAP2 WILD-TYPE 
          70.55          223.96 
  GRAP2 MUTATED GRAP2 WILD-TYPE 
          12.54           18.10 
[1] "0.3 - 70.5 (12.5)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D122V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GRAP2 MUTATED         0        5        4         0         0          1
  GRAP2 WILD-TYPE       4      118      129        46        67         69
                 vv
clus              STAGE IIIB STAGE IV
  GRAP2 MUTATED            0        1
  GRAP2 WILD-TYPE         11       24
D122V3, multiclass
            clus
vv           GRAP2 MUTATED GRAP2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRAP2 MUTATED     5   6   0   0
  GRAP2 WILD-TYPE 150 255  43  18
D122V4, multiclass
    clus
vv   GRAP2 MUTATED GRAP2 WILD-TYPE
  T1             5             150
  T2             6             255
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  GRAP2 MUTATED     9   1     1
  GRAP2 WILD-TYPE 298  88    71
D122V5, multiclass
       clus
vv      GRAP2 MUTATED GRAP2 WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             1              71
[1] 3 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
  GRAP2 MUTATED     8   1
  GRAP2 WILD-TYPE 319  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRAP2 MUTATED      8    1
  GRAP2 WILD-TYPE  319   22
   clus
vv  GRAP2 MUTATED GRAP2 WILD-TYPE
  0             8             319
  1             1              22
[1] 2 2
[1] FALSE
D122V7, binary
                 cls
clus                0   1
  GRAP2 MUTATED     1  10
  GRAP2 WILD-TYPE 258 211
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRAP2 MUTATED      1   10
  GRAP2 WILD-TYPE  258  211
        clus
vv       GRAP2 MUTATED GRAP2 WILD-TYPE
  FEMALE             1             258
  MALE              10             211
[1] 2 2
[1] FALSE
D122V8, continuous
[1] "Remove cluster labels:" "GRAP2 MUTATED"         
clus
  GRAP2 MUTATED GRAP2 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"GRAP2 WILD-TYPE" "GRAP2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GRAP2 MUTATED                            1                                 2
  GRAP2 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GRAP2 MUTATED                                                    6
  GRAP2 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GRAP2 MUTATED                                            0
  GRAP2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GRAP2 MUTATED                                               1
  GRAP2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  GRAP2 MUTATED                                0
  GRAP2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  GRAP2 MUTATED                                    0
  GRAP2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GRAP2 MUTATED                              0                             1
  GRAP2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GRAP2 MUTATED                                               0
  GRAP2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  GRAP2 MUTATED                              0
  GRAP2 WILD-TYPE                            9
D122V9, multiclass
                                                    clus
vv                                                   GRAP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   GRAP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V10, binary
                 cls
clus                0   1
  GRAP2 MUTATED     2   9
  GRAP2 WILD-TYPE  18 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRAP2 MUTATED      2    9
  GRAP2 WILD-TYPE   18  451
     clus
vv    GRAP2 MUTATED GRAP2 WILD-TYPE
  NO              2              18
  YES             9             451
[1] 2 2
[1] FALSE
D122V11, continuous
D122V12, continuous
                 vv
clus               R0  R1  R2  RX
  GRAP2 MUTATED     5   0   0   1
  GRAP2 WILD-TYPE 305  11   4  24
D122V13, multiclass
    clus
vv   GRAP2 MUTATED GRAP2 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRAP2 MUTATED                                  0     0
  GRAP2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRAP2 MUTATED                           1     9
  GRAP2 WILD-TYPE                        28   368
D122V14, multiclass
                                  clus
vv                                 GRAP2 MUTATED GRAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V15, binary
                 cls
clus                0   1
  GRAP2 MUTATED     0  10
  GRAP2 WILD-TYPE   6 339
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRAP2 MUTATED      0   10
  GRAP2 WILD-TYPE    6  339
                        clus
vv                       GRAP2 MUTATED GRAP2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            10             339
[1] 2 2
[1] FALSE

Clustering(123) Variable = ARHGAP4 MUTATION ANALYSIS
D123V1, survival
                   sevent
clus2                 0   1
  ARHGAP4 MUTATED    12   2
  ARHGAP4 WILD-TYPE 303 139
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
               14               442 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2               139 
$`ARHGAP4 MUTATED`
TCGA-44-5644 TCGA-44-8117 TCGA-50-5935 TCGA-55-6543 TCGA-55-6970 TCGA-55-7281 
       28.37        12.66        21.47         0.07        15.25         0.59 
TCGA-55-7724 TCGA-55-7994 TCGA-55-7995 TCGA-55-A490 TCGA-55-A492 TCGA-78-7163 
       23.18        19.82         0.16         1.58        19.59       223.96 
TCGA-86-8075 TCGA-95-7043 
       15.75         1.22 

$`ARHGAP4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
       36.07        18.87        29.00        17.59        23.64         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        78.67         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         2.86        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         1.74         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         3.12         1.32         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       17.65         6.15        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       21.40        20.58         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
       64.90        22.29         7.07       104.19         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57        24.33         0.79        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
             0.07              0.00 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
           223.96            214.62 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
             15.5              18.1 
[1] "0.1 - 224.0 (15.5)" "0.0 - 214.6 (18.1)"
[1] "hr=" "2.1"
D123V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARHGAP4 MUTATED         0        6        5         1         1          1
  ARHGAP4 WILD-TYPE       4      117      128        45        66         69
                   vv
clus                STAGE IIIB STAGE IV
  ARHGAP4 MUTATED            0        0
  ARHGAP4 WILD-TYPE         11       25
D123V3, multiclass
            clus
vv           ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 6               117
  STAGE IB                 5               128
  STAGE IIA                1                45
  STAGE IIB                1                66
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGAP4 MUTATED     6   7   1   0
  ARHGAP4 WILD-TYPE 149 254  42  18
D123V4, multiclass
    clus
vv   ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  T1               6               149
  T2               7               254
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  ARHGAP4 MUTATED    13   0     1
  ARHGAP4 WILD-TYPE 294  89    71
D123V5, multiclass
       clus
vv      ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  N0                 13               294
  N1                  0                89
  N2+N3               1                71
[1] 3 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
  ARHGAP4 MUTATED     6   0
  ARHGAP4 WILD-TYPE 321  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      6    0
  ARHGAP4 WILD-TYPE  321   23
   clus
vv  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  0               6               321
  1               0                23
[1] 2 2
[1] FALSE
D123V7, binary
                   cls
clus                  0   1
  ARHGAP4 MUTATED    11   3
  ARHGAP4 WILD-TYPE 248 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED     11    3
  ARHGAP4 WILD-TYPE  248  218
        clus
vv       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  FEMALE              11               248
  MALE                 3               218
[1] 2 2
[1] FALSE
D123V8, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8076        TCGA-86-8278 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8281        TCGA-86-8358        TCGA-86-8359 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-86-8668        TCGA-86-8669        TCGA-86-8671        TCGA-86-A4JF 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ARHGAP4 MUTATED                            0
  ARHGAP4 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARHGAP4 MUTATED                                   1
  ARHGAP4 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP4 MUTATED                                                   11
  ARHGAP4 WILD-TYPE                                                283
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARHGAP4 MUTATED                                            1
  ARHGAP4 WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARHGAP4 MUTATED                                               0
  ARHGAP4 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ARHGAP4 MUTATED                                0
  ARHGAP4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ARHGAP4 MUTATED                                    0
  ARHGAP4 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARHGAP4 MUTATED                              0                             1
  ARHGAP4 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARHGAP4 MUTATED                                               0
  ARHGAP4 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ARHGAP4 MUTATED                              0
  ARHGAP4 WILD-TYPE                            9
D123V9, multiclass
                                                    clus
vv                                                   ARHGAP4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ARHGAP4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V10, binary
                   cls
clus                  0   1
  ARHGAP4 MUTATED     1  13
  ARHGAP4 WILD-TYPE  19 447
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      1   13
  ARHGAP4 WILD-TYPE   19  447
     clus
vv    ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  NO                1                19
  YES              13               447
[1] 2 2
[1] FALSE
D123V11, continuous
D123V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ARHGAP4 MUTATED     8   1   0   0
  ARHGAP4 WILD-TYPE 302  10   4  25
D123V13, multiclass
    clus
vv   ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  R0               8               302
  R1               1                10
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP4 MUTATED                                  0     0
  ARHGAP4 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP4 MUTATED                           0    14
  ARHGAP4 WILD-TYPE                        29   363
D123V14, multiclass
                                  clus
vv                                 ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                         14               363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V15, binary
                   cls
clus                  0   1
  ARHGAP4 MUTATED     0  10
  ARHGAP4 WILD-TYPE   6 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      0   10
  ARHGAP4 WILD-TYPE    6  339
                        clus
vv                       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              10               339
[1] 2 2
[1] FALSE

Clustering(124) Variable = IFI35 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2               0   1
  IFI35 MUTATED     2   1
  IFI35 WILD-TYPE 313 140
  IFI35 MUTATED IFI35 WILD-TYPE 
              3             453 
  IFI35 MUTATED IFI35 WILD-TYPE 
              1             140 
$`IFI35 MUTATED`
TCGA-55-8301 TCGA-78-8660 TCGA-95-7948 
        1.45        10.55        15.65 

$`IFI35 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       32.68       214.62        39.75        77.59       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.68        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  IFI35 MUTATED IFI35 WILD-TYPE 
           1.45            0.00 
  IFI35 MUTATED IFI35 WILD-TYPE 
          15.65          223.96 
  IFI35 MUTATED IFI35 WILD-TYPE 
          10.55           18.12 
[1] "1.4 - 15.7 (10.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "3.3"
D124V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IFI35 MUTATED         0        0        2         0         1          0
  IFI35 WILD-TYPE       4      123      131        46        66         70
                 vv
clus              STAGE IIIB STAGE IV
  IFI35 MUTATED            0        0
  IFI35 WILD-TYPE         11       25
D124V3, multiclass
            clus
vv           IFI35 MUTATED IFI35 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               2             131
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFI35 MUTATED     0   3   0   0
  IFI35 WILD-TYPE 155 258  43  18
D124V4, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  T1             0             155
  T2             3             258
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  IFI35 MUTATED     2   1     0
  IFI35 WILD-TYPE 305  88    72
D124V5, multiclass
       clus
vv      IFI35 MUTATED IFI35 WILD-TYPE
  N0                2             305
  N1                1              88
  N2+N3             0              72
[1] 3 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
  IFI35 MUTATED     2   0
  IFI35 WILD-TYPE 325  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      2    0
  IFI35 WILD-TYPE  325   23
   clus
vv  IFI35 MUTATED IFI35 WILD-TYPE
  0             2             325
  1             0              23
[1] 2 2
[1] FALSE
D124V7, binary
                 cls
clus                0   1
  IFI35 MUTATED     1   2
  IFI35 WILD-TYPE 258 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      1    2
  IFI35 WILD-TYPE  258  219
        clus
vv       IFI35 MUTATED IFI35 WILD-TYPE
  FEMALE             1             258
  MALE               2             219
[1] 2 2
[1] FALSE
D124V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  IFI35 MUTATED                            0                                 1
  IFI35 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IFI35 MUTATED                                                    2
  IFI35 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IFI35 MUTATED                                            0
  IFI35 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IFI35 MUTATED                                               0
  IFI35 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  IFI35 MUTATED                                0
  IFI35 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  IFI35 MUTATED                                    0
  IFI35 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  IFI35 MUTATED                              0                             0
  IFI35 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IFI35 MUTATED                                               0
  IFI35 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  IFI35 MUTATED                              0
  IFI35 WILD-TYPE                            9
D124V9, multiclass
                                                    clus
vv                                                   IFI35 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   IFI35 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V10, binary
                 cls
clus                0   1
  IFI35 MUTATED     0   3
  IFI35 WILD-TYPE  20 457
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      0    3
  IFI35 WILD-TYPE   20  457
     clus
vv    IFI35 MUTATED IFI35 WILD-TYPE
  NO              0              20
  YES             3             457
[1] 2 2
[1] FALSE
D124V11, continuous
D124V12, continuous
                 vv
clus               R0  R1  R2  RX
  IFI35 MUTATED     3   0   0   0
  IFI35 WILD-TYPE 307  11   4  25
D124V13, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFI35 MUTATED                                  0     0
  IFI35 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFI35 MUTATED                           0     2
  IFI35 WILD-TYPE                        29   375
D124V14, multiclass
[1] "Remove cluster labels:" "IFI35 MUTATED"         
clus
  IFI35 MUTATED IFI35 WILD-TYPE 
              2             412 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-38-4625 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-38-4626      TCGA-38-4627      TCGA-38-4628      TCGA-38-4629 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-38-4630      TCGA-38-4631      TCGA-38-4632      TCGA-38-6178 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-2661      TCGA-44-2665      TCGA-44-3396      TCGA-44-3398 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-3919      TCGA-44-4112      TCGA-44-5643 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-5644      TCGA-44-5645      TCGA-44-6144      TCGA-44-6145 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-6146      TCGA-44-6147      TCGA-44-6148      TCGA-44-6774 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-6776      TCGA-44-6777      TCGA-44-6778 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-6779      TCGA-44-7659      TCGA-44-7660      TCGA-44-7661 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-7662      TCGA-44-7667      TCGA-44-7669      TCGA-44-7670 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-7671      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4488      TCGA-49-4490 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4501      TCGA-49-4505      TCGA-49-4506 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-49-4507      TCGA-49-4510      TCGA-49-4512      TCGA-49-4514 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-49-6745 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-49-6761      TCGA-49-6767      TCGA-50-5044      TCGA-50-5045 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-5049      TCGA-50-5051      TCGA-50-5055      TCGA-50-5066 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-5068      TCGA-50-5072      TCGA-50-5930      TCGA-50-5931 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-5932      TCGA-50-5933      TCGA-50-5935      TCGA-50-5936 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-5939      TCGA-50-5941      TCGA-50-5942      TCGA-50-5944 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-5946      TCGA-50-6590      TCGA-50-6591      TCGA-50-6592 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-6593      TCGA-50-6594      TCGA-50-6595      TCGA-50-6597 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-6673      TCGA-50-7109      TCGA-50-8457      TCGA-50-8459 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-50-8460      TCGA-53-7624      TCGA-53-7626      TCGA-53-7813 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-1592      TCGA-55-1595      TCGA-55-5899 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-6543      TCGA-55-6642      TCGA-55-6712      TCGA-55-6968 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-6969      TCGA-55-6970      TCGA-55-6971      TCGA-55-6972 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-6975      TCGA-55-6978      TCGA-55-6979      TCGA-55-6980 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-6981      TCGA-55-6982      TCGA-55-6983      TCGA-55-6984 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-6985      TCGA-55-6986      TCGA-55-6987      TCGA-55-7227 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-7281      TCGA-55-7283      TCGA-55-7284      TCGA-55-7570 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7727      TCGA-55-7816 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-7903      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-7994      TCGA-55-7995      TCGA-55-8085 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8087      TCGA-55-8089      TCGA-55-8090      TCGA-55-8091 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8203      TCGA-55-8204      TCGA-55-8205      TCGA-55-8206 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8207      TCGA-55-8208      TCGA-55-8299      TCGA-55-8302 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8505      TCGA-55-8506      TCGA-55-8507      TCGA-55-8508 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8510      TCGA-55-8511      TCGA-55-8512      TCGA-55-8513 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8614      TCGA-55-8615      TCGA-55-8616 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-55-A4DG      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1676      TCGA-64-1677      TCGA-64-1679 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5774      TCGA-64-5775      TCGA-64-5778 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-64-5779      TCGA-64-5781      TCGA-64-5815      TCGA-67-3771 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-67-3772      TCGA-67-3773      TCGA-67-4679      TCGA-67-6215 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-67-6216      TCGA-67-6217      TCGA-69-7760      TCGA-69-7761 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-69-7763      TCGA-69-7764      TCGA-69-7765      TCGA-69-7973 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7978      TCGA-69-7979      TCGA-69-7980 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-69-8253      TCGA-69-8254      TCGA-69-8255      TCGA-69-A59K 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4658      TCGA-73-4659 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-4677      TCGA-73-7498 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-73-7499      TCGA-78-7143      TCGA-78-7145      TCGA-78-7146 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-78-7147      TCGA-78-7148      TCGA-78-7149      TCGA-78-7150 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-78-7152      TCGA-78-7153      TCGA-78-7154      TCGA-78-7155 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-78-7156      TCGA-78-7158      TCGA-78-7159      TCGA-78-7160 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-78-7161      TCGA-78-7162      TCGA-78-7163      TCGA-78-7166 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-78-7167      TCGA-78-7220      TCGA-78-7535      TCGA-78-7536 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-78-7539      TCGA-78-7540      TCGA-78-7542      TCGA-78-7633 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6562      TCGA-86-6851      TCGA-86-7701 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7713      TCGA-86-7714      TCGA-86-7953 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8054      TCGA-86-8055 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8075 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8358      TCGA-86-8359      TCGA-86-8585 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-8672 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-8673      TCGA-86-8674      TCGA-86-A456      TCGA-86-A4JF 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-86-A4P8      TCGA-91-6828      TCGA-91-6829 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-91-6830      TCGA-91-6831      TCGA-91-6835      TCGA-91-6836 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-91-6840      TCGA-91-6847      TCGA-91-6848      TCGA-91-6849 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-91-7771      TCGA-91-8496      TCGA-91-8497      TCGA-91-8499 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-91-A4BD      TCGA-93-7347      TCGA-93-7348 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JP 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-93-A4JQ      TCGA-95-7039      TCGA-95-7043      TCGA-95-7562 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-95-7567      TCGA-95-7944      TCGA-95-7947      TCGA-95-8039 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-95-8494      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7547      TCGA-97-7552      TCGA-97-7553 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-97-7554      TCGA-97-7937      TCGA-97-7938      TCGA-97-7941 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8175 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-97-8176      TCGA-97-8177      TCGA-97-8179      TCGA-97-8552 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M6      TCGA-97-A4M7 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-99-8033      TCGA-J2-8192      TCGA-J2-8194      TCGA-J2-A4AD 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-J2-A4AE      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SW      TCGA-MP-A4SY      TCGA-MP-A4T2 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T9      TCGA-MP-A4TA 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-MP-A4TC      TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TF 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A5C7      TCGA-NJ-A4YF 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
     TCGA-NJ-A55A      TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" "IFI35 WILD-TYPE" 
D124V15, binary
                 cls
clus                0   1
  IFI35 MUTATED     0   2
  IFI35 WILD-TYPE   6 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      0    2
  IFI35 WILD-TYPE    6  347
                        clus
vv                       IFI35 MUTATED IFI35 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2             347
[1] 2 2
[1] FALSE

Clustering(125) Variable = CDK12 MUTATION ANALYSIS
D125V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED     8   6
  CDK12 WILD-TYPE 307 135
  CDK12 MUTATED CDK12 WILD-TYPE 
             14             442 
  CDK12 MUTATED CDK12 WILD-TYPE 
              6             135 
$`CDK12 MUTATED`
TCGA-05-4397 TCGA-35-4122 TCGA-38-4628 TCGA-44-7660 TCGA-44-8119 TCGA-44-8120 
       24.03         7.40        49.05        19.46         3.25         8.55 
TCGA-50-5930 TCGA-50-5939 TCGA-55-8089 TCGA-62-A46O TCGA-64-1679 TCGA-78-7154 
        9.27        15.12         3.29        47.80        55.43        19.50 
TCGA-99-8032 TCGA-L9-A444 
        1.45         0.20 

$`CDK12 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       14.60        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       17.59        23.64        12.66        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 
       14.27        40.60        78.67        21.47         8.45        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 
       16.44        19.00        14.30         3.81        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  CDK12 MUTATED CDK12 WILD-TYPE 
            0.2             0.0 
  CDK12 MUTATED CDK12 WILD-TYPE 
          55.43          223.96 
  CDK12 MUTATED CDK12 WILD-TYPE 
         12.195          18.100 
[1] "0.2 - 55.4 (12.2)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.7"
D125V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CDK12 MUTATED         0        4        4         0         3          3
  CDK12 WILD-TYPE       4      119      129        46        64         67
                 vv
clus              STAGE IIIB STAGE IV
  CDK12 MUTATED            0        1
  CDK12 WILD-TYPE         11       24
D125V3, multiclass
            clus
vv           CDK12 MUTATED CDK12 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK12 MUTATED     5   8   2   0
  CDK12 WILD-TYPE 150 253  41  18
D125V4, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T1             5             150
  T2             8             253
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  CDK12 MUTATED     9   2     4
  CDK12 WILD-TYPE 298  87    68
D125V5, multiclass
       clus
vv      CDK12 MUTATED CDK12 WILD-TYPE
  N0                9             298
  N1                2              87
  N2+N3             4              68
[1] 3 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
  CDK12 MUTATED    12   1
  CDK12 WILD-TYPE 315  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     12    1
  CDK12 WILD-TYPE  315   22
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0            12             315
  1             1              22
[1] 2 2
[1] FALSE
D125V7, binary
                 cls
clus                0   1
  CDK12 MUTATED     4  11
  CDK12 WILD-TYPE 255 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      4   11
  CDK12 WILD-TYPE  255  210
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  FEMALE             4             255
  MALE              11             210
[1] 2 2
[1] FALSE
D125V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CDK12 MUTATED                            0                                 3
  CDK12 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDK12 MUTATED                                                   12
  CDK12 WILD-TYPE                                                282
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CDK12 MUTATED                                            0
  CDK12 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CDK12 MUTATED                                               0
  CDK12 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CDK12 MUTATED                                0
  CDK12 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CDK12 MUTATED                                    0
  CDK12 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CDK12 MUTATED                              0                             0
  CDK12 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CDK12 MUTATED                                               0
  CDK12 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CDK12 MUTATED                              0
  CDK12 WILD-TYPE                            9
D125V9, multiclass
                                                    clus
vv                                                   CDK12 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CDK12 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V10, binary
                 cls
clus                0   1
  CDK12 MUTATED     1  14
  CDK12 WILD-TYPE  19 446
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      1   14
  CDK12 WILD-TYPE   19  446
     clus
vv    CDK12 MUTATED CDK12 WILD-TYPE
  NO              1              19
  YES            14             446
[1] 2 2
[1] FALSE
D125V11, continuous
D125V12, continuous
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED     9   0   0   1
  CDK12 WILD-TYPE 301  11   4  24
D125V13, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK12 MUTATED                                  0     0
  CDK12 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED                           1    12
  CDK12 WILD-TYPE                        28   365
D125V14, multiclass
                                  clus
vv                                 CDK12 MUTATED CDK12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V15, binary
                 cls
clus                0   1
  CDK12 MUTATED     0  12
  CDK12 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      0   12
  CDK12 WILD-TYPE    6  337
                        clus
vv                       CDK12 MUTATED CDK12 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(126) Variable = TMEM202 MUTATION ANALYSIS
D126V1, survival
                   sevent
clus2                 0   1
  TMEM202 MUTATED     3   3
  TMEM202 WILD-TYPE 312 138
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                6               450 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                3               138 
$`TMEM202 MUTATED`
TCGA-05-4384 TCGA-38-4631 TCGA-44-8119 TCGA-55-7724 TCGA-78-8660 TCGA-86-7711 
       14.01        11.64         3.25        23.18        10.55        34.39 

$`TMEM202 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       18.87        29.00        17.59        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  TMEM202 MUTATED TMEM202 WILD-TYPE 
             3.25              0.00 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
            34.39            223.96 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
           12.825            18.100 
[1] "3.2 - 34.4 (12.8)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.7"
D126V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TMEM202 MUTATED         0        0        2         1         2          1
  TMEM202 WILD-TYPE       4      123      131        45        65         69
                   vv
clus                STAGE IIIB STAGE IV
  TMEM202 MUTATED            0        0
  TMEM202 WILD-TYPE         11       25
D126V3, multiclass
            clus
vv           TMEM202 MUTATED TMEM202 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0               123
  STAGE IB                 2               131
  STAGE IIA                1                45
  STAGE IIB                2                65
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM202 MUTATED     0   5   1   0
  TMEM202 WILD-TYPE 155 256  42  18
D126V4, multiclass
    clus
vv   TMEM202 MUTATED TMEM202 WILD-TYPE
  T1               0               155
  T2               5               256
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  TMEM202 MUTATED     3   2     1
  TMEM202 WILD-TYPE 304  87    71
D126V5, multiclass
       clus
vv      TMEM202 MUTATED TMEM202 WILD-TYPE
  N0                  3               304
  N1                  2                87
  N2+N3               1                71
[1] 3 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
  TMEM202 MUTATED     5   0
  TMEM202 WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM202 MUTATED      5    0
  TMEM202 WILD-TYPE  322   23
   clus
vv  TMEM202 MUTATED TMEM202 WILD-TYPE
  0               5               322
  1               0                23
[1] 2 2
[1] FALSE
D126V7, binary
                   cls
clus                  0   1
  TMEM202 MUTATED     2   4
  TMEM202 WILD-TYPE 257 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM202 MUTATED      2    4
  TMEM202 WILD-TYPE  257  217
        clus
vv       TMEM202 MUTATED TMEM202 WILD-TYPE
  FEMALE               2               257
  MALE                 4               217
[1] 2 2
[1] FALSE
D126V8, continuous
[1] "Remove cluster labels:" "TMEM202 MUTATED"       
clus
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7713 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  TMEM202 MUTATED                            0
  TMEM202 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  TMEM202 MUTATED                                   1
  TMEM202 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TMEM202 MUTATED                                                    5
  TMEM202 WILD-TYPE                                                289
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TMEM202 MUTATED                                            0
  TMEM202 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TMEM202 MUTATED                                               0
  TMEM202 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  TMEM202 MUTATED                                0
  TMEM202 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  TMEM202 MUTATED                                    0
  TMEM202 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TMEM202 MUTATED                              0                             0
  TMEM202 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TMEM202 MUTATED                                               0
  TMEM202 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  TMEM202 MUTATED                              0
  TMEM202 WILD-TYPE                            9
D126V9, multiclass
                                                    clus
vv                                                   TMEM202 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   TMEM202 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V10, binary
                   cls
clus                  0   1
  TMEM202 MUTATED     0   6
  TMEM202 WILD-TYPE  20 454
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM202 MUTATED      0    6
  TMEM202 WILD-TYPE   20  454
     clus
vv    TMEM202 MUTATED TMEM202 WILD-TYPE
  NO                0                20
  YES               6               454
[1] 2 2
[1] FALSE
D126V11, continuous
D126V12, continuous
                   vv
clus                 R0  R1  R2  RX
  TMEM202 MUTATED     4   0   0   1
  TMEM202 WILD-TYPE 306  11   4  24
D126V13, multiclass
    clus
vv   TMEM202 MUTATED TMEM202 WILD-TYPE
  R0               4               306
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM202 MUTATED                                  0     0
  TMEM202 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM202 MUTATED                           0     4
  TMEM202 WILD-TYPE                        29   373
D126V14, multiclass
                                  clus
vv                                 TMEM202 MUTATED TMEM202 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          4               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V15, binary
                   cls
clus                  0   1
  TMEM202 MUTATED     1   3
  TMEM202 WILD-TYPE   5 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM202 MUTATED      1    3
  TMEM202 WILD-TYPE    5  346
                        clus
vv                       TMEM202 MUTATED TMEM202 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               3               346
[1] 2 2
[1] FALSE

Clustering(127) Variable = GTF2A1 MUTATION ANALYSIS
D127V1, survival
                  sevent
clus2                0   1
  GTF2A1 MUTATED     1   2
  GTF2A1 WILD-TYPE 314 139
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
               3              453 
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
               2              139 
$`GTF2A1 MUTATED`
TCGA-05-4424 TCGA-95-7562 TCGA-97-8174 
       30.02         2.86         5.39 

$`GTF2A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         1.22        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        5.95         0.59         0.72        18.67        17.92        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
            2.86             0.00 
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
           30.02           223.96 
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
            5.39            18.08 
[1] "2.9 - 30.0 (5.4)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "4.5"
D127V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GTF2A1 MUTATED         0        0        0         2         1          0
  GTF2A1 WILD-TYPE       4      123      133        44        66         70
                  vv
clus               STAGE IIIB STAGE IV
  GTF2A1 MUTATED            0        0
  GTF2A1 WILD-TYPE         11       25
D127V3, multiclass
            clus
vv           GTF2A1 MUTATED GTF2A1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0              123
  STAGE IB                0              133
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GTF2A1 MUTATED     0   2   1   0
  GTF2A1 WILD-TYPE 155 259  42  18
D127V4, multiclass
    clus
vv   GTF2A1 MUTATED GTF2A1 WILD-TYPE
  T1              0              155
  T2              2              259
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  GTF2A1 MUTATED     2   1     0
  GTF2A1 WILD-TYPE 305  88    72
D127V5, multiclass
       clus
vv      GTF2A1 MUTATED GTF2A1 WILD-TYPE
  N0                 2              305
  N1                 1               88
  N2+N3              0               72
[1] 3 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
  GTF2A1 MUTATED     3   0
  GTF2A1 WILD-TYPE 324  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2A1 MUTATED      3    0
  GTF2A1 WILD-TYPE  324   23
   clus
vv  GTF2A1 MUTATED GTF2A1 WILD-TYPE
  0              3              324
  1              0               23
[1] 2 2
[1] FALSE
D127V7, binary
                  cls
clus                 0   1
  GTF2A1 MUTATED     0   3
  GTF2A1 WILD-TYPE 259 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2A1 MUTATED      0    3
  GTF2A1 WILD-TYPE  259  218
        clus
vv       GTF2A1 MUTATED GTF2A1 WILD-TYPE
  FEMALE              0              259
  MALE                3              218
[1] 2 2
[1] FALSE
D127V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GTF2A1 MUTATED                            0                                 1
  GTF2A1 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GTF2A1 MUTATED                                                    1
  GTF2A1 WILD-TYPE                                                293
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GTF2A1 MUTATED                                            0
  GTF2A1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GTF2A1 MUTATED                                               0
  GTF2A1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  GTF2A1 MUTATED                                0
  GTF2A1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  GTF2A1 MUTATED                                    0
  GTF2A1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GTF2A1 MUTATED                              0                             1
  GTF2A1 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GTF2A1 MUTATED                                               0
  GTF2A1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  GTF2A1 MUTATED                              0
  GTF2A1 WILD-TYPE                            9
D127V9, multiclass
                                                    clus
vv                                                   GTF2A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   GTF2A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V10, binary
                  cls
clus                 0   1
  GTF2A1 MUTATED     0   3
  GTF2A1 WILD-TYPE  20 457
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2A1 MUTATED      0    3
  GTF2A1 WILD-TYPE   20  457
     clus
vv    GTF2A1 MUTATED GTF2A1 WILD-TYPE
  NO               0               20
  YES              3              457
[1] 2 2
[1] FALSE
D127V11, continuous
D127V12, continuous
                  vv
clus                R0  R1  R2  RX
  GTF2A1 MUTATED     0   1   0   1
  GTF2A1 WILD-TYPE 310  10   4  24
D127V13, multiclass
[1] "Remove cluster labels:" "GTF2A1 MUTATED"        
clus
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
               2              348 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-05-4382 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-4384       TCGA-05-4389       TCGA-05-4390       TCGA-05-4395 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-4396       TCGA-05-4397       TCGA-05-4398       TCGA-05-4402 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-4403       TCGA-05-4405       TCGA-05-4410       TCGA-05-4415 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-4417       TCGA-05-4418       TCGA-05-4420       TCGA-05-4422 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-4425       TCGA-05-4426       TCGA-05-4427       TCGA-05-4430 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-4432       TCGA-05-4433       TCGA-05-4434       TCGA-05-5420 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-5423       TCGA-05-5425       TCGA-05-5428       TCGA-05-5429 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-05-5715       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-38-4625       TCGA-38-4626       TCGA-38-4627       TCGA-38-4628 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-38-4629       TCGA-38-4630       TCGA-38-4631       TCGA-38-4632 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-38-6178       TCGA-38-7271       TCGA-38-A44F       TCGA-44-2657 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-2661       TCGA-44-2665       TCGA-44-3396       TCGA-44-3398 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-44-6144 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-6148       TCGA-44-6775       TCGA-44-A479       TCGA-44-A47A 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SU       TCGA-49-4486 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-4487       TCGA-49-4488       TCGA-49-4494       TCGA-49-4501 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-4505       TCGA-49-4506       TCGA-49-4507       TCGA-49-4510 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-4512       TCGA-49-4514       TCGA-49-6742       TCGA-49-6744 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-6761       TCGA-49-6767       TCGA-50-5051       TCGA-50-5055 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-5066       TCGA-50-5931       TCGA-50-5942       TCGA-50-5944 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-6593       TCGA-50-6597       TCGA-50-6673       TCGA-50-8460 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-53-7624       TCGA-53-7626       TCGA-53-A4EZ       TCGA-55-1592 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-5899       TCGA-55-6642       TCGA-55-6970       TCGA-55-6971 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-6972       TCGA-55-6980       TCGA-55-6981       TCGA-55-6983 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-6985       TCGA-55-7281       TCGA-55-7284       TCGA-55-7570 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7574       TCGA-55-7576       TCGA-55-7724       TCGA-55-7725 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7727       TCGA-55-7728       TCGA-55-7815 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7903       TCGA-55-7907       TCGA-55-7910       TCGA-55-7911 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-7994       TCGA-55-7995       TCGA-55-8085 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8087       TCGA-55-8089       TCGA-55-8090       TCGA-55-8091 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8097       TCGA-55-8203 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8204       TCGA-55-8205       TCGA-55-8206       TCGA-55-8207 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8299       TCGA-55-8301       TCGA-55-8302 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8505       TCGA-55-8506       TCGA-55-8507       TCGA-55-8508 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8510       TCGA-55-8511       TCGA-55-8512       TCGA-55-8513 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8514       TCGA-55-8614       TCGA-55-8615       TCGA-55-8616 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-8621       TCGA-55-A48X 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A493       TCGA-55-A494       TCGA-55-A4DF 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1676       TCGA-64-1677       TCGA-64-1679 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5774       TCGA-64-5775       TCGA-64-5778 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-64-5779       TCGA-64-5781       TCGA-64-5815       TCGA-67-3771 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-67-3773       TCGA-67-4679       TCGA-67-6215       TCGA-67-6216 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-67-6217       TCGA-71-6725       TCGA-71-8520       TCGA-73-4658 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4675       TCGA-73-4676       TCGA-73-4677 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-75-5125 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-75-5126       TCGA-75-5146       TCGA-75-5147       TCGA-75-6203 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-75-6205       TCGA-75-6206       TCGA-75-6207       TCGA-75-6211 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-75-6212       TCGA-75-6214       TCGA-75-7025       TCGA-75-7027 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-75-7030       TCGA-75-7031       TCGA-78-7143       TCGA-78-7145 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7146       TCGA-78-7147       TCGA-78-7148       TCGA-78-7149 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7150       TCGA-78-7152       TCGA-78-7153       TCGA-78-7154 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7155       TCGA-78-7156       TCGA-78-7158       TCGA-78-7159 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7160       TCGA-78-7161       TCGA-78-7162       TCGA-78-7163 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7167       TCGA-78-7220       TCGA-78-7535 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7536       TCGA-78-7537       TCGA-78-7539       TCGA-78-7540 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7542       TCGA-78-7633       TCGA-78-8640       TCGA-78-8648 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-8655       TCGA-78-8660       TCGA-78-8662       TCGA-80-5607 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-80-5608       TCGA-80-5611       TCGA-83-5908       TCGA-86-6562 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-7953       TCGA-86-7954       TCGA-86-7955       TCGA-86-8054 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8073       TCGA-86-8074 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8075       TCGA-86-8076       TCGA-86-8278       TCGA-86-8279 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8280       TCGA-86-8358       TCGA-86-8359       TCGA-86-8585 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-8672 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8673       TCGA-86-8674       TCGA-86-A456       TCGA-86-A4JF 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6828       TCGA-91-6829       TCGA-91-6835 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-91-6840       TCGA-91-A4BD       TCGA-93-7347       TCGA-93-7348 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JP 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-93-A4JQ       TCGA-95-7944       TCGA-95-7947       TCGA-95-7948 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-95-8039       TCGA-95-A4VK       TCGA-95-A4VN       TCGA-97-7546 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-97-7554       TCGA-97-7938       TCGA-97-7941       TCGA-97-8176 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M7       TCGA-99-7458       TCGA-99-8025 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-99-8028       TCGA-99-8032       TCGA-99-8033       TCGA-J2-A4AD 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-J2-A4AE       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1       TCGA-MN-A4N4 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T7 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MP-A4T8       TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MP-A4TI       TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YQ 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2A1 MUTATED                                  0     0
  GTF2A1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GTF2A1 MUTATED                           1     1
  GTF2A1 WILD-TYPE                        28   376
D127V14, multiclass
[1] "Remove cluster labels:" "GTF2A1 MUTATED"        
clus
  GTF2A1 MUTATED GTF2A1 WILD-TYPE 
               2              412 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-38-4625 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-38-4626       TCGA-38-4627       TCGA-38-4628       TCGA-38-4629 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-38-4630       TCGA-38-4631       TCGA-38-4632       TCGA-38-6178 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-38-7271       TCGA-38-A44F       TCGA-44-2656       TCGA-44-2657 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-2661       TCGA-44-2665       TCGA-44-3396       TCGA-44-3398 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-44-5643 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-5644       TCGA-44-5645       TCGA-44-6144       TCGA-44-6145 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-6146       TCGA-44-6147       TCGA-44-6148       TCGA-44-6774 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-6776       TCGA-44-6777       TCGA-44-6778 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-6779       TCGA-44-7659       TCGA-44-7660       TCGA-44-7661 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-7662       TCGA-44-7667       TCGA-44-7669       TCGA-44-7670 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-7671       TCGA-44-7672       TCGA-44-8117       TCGA-44-8119 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-44-A47F       TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4488       TCGA-49-4490 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-4494       TCGA-49-4501       TCGA-49-4505       TCGA-49-4506 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-4507       TCGA-49-4510       TCGA-49-4512       TCGA-49-4514 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-49-6745 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-49-6761       TCGA-49-6767       TCGA-50-5044       TCGA-50-5045 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-5049       TCGA-50-5051       TCGA-50-5055       TCGA-50-5066 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-5068       TCGA-50-5072       TCGA-50-5930       TCGA-50-5931 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-5932       TCGA-50-5933       TCGA-50-5935       TCGA-50-5936 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-5939       TCGA-50-5941       TCGA-50-5942       TCGA-50-5944 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-5946       TCGA-50-6590       TCGA-50-6591       TCGA-50-6592 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-6593       TCGA-50-6594       TCGA-50-6595       TCGA-50-6597 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-6673       TCGA-50-7109       TCGA-50-8457       TCGA-50-8459 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-50-8460       TCGA-53-7624       TCGA-53-7626       TCGA-53-7813 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-1592       TCGA-55-1595       TCGA-55-5899 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-6543       TCGA-55-6642       TCGA-55-6712       TCGA-55-6968 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-6969       TCGA-55-6970       TCGA-55-6971       TCGA-55-6972 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-6975       TCGA-55-6978       TCGA-55-6979       TCGA-55-6980 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-6981       TCGA-55-6982       TCGA-55-6983       TCGA-55-6984 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-6985       TCGA-55-6986       TCGA-55-6987       TCGA-55-7227 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7281       TCGA-55-7283       TCGA-55-7284       TCGA-55-7570 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7573       TCGA-55-7574       TCGA-55-7576       TCGA-55-7724 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7727       TCGA-55-7816 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7903       TCGA-55-7907       TCGA-55-7910       TCGA-55-7911 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-7994       TCGA-55-7995       TCGA-55-8085 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8087       TCGA-55-8089       TCGA-55-8090       TCGA-55-8091 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8096       TCGA-55-8097 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8206 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8207       TCGA-55-8208       TCGA-55-8299       TCGA-55-8301 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8302       TCGA-55-8505       TCGA-55-8506       TCGA-55-8507 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8510       TCGA-55-8511       TCGA-55-8512 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8513       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-8616       TCGA-55-8619       TCGA-55-8620       TCGA-55-8621 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A493       TCGA-55-A494 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-55-A4DF       TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1676       TCGA-64-1677 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-64-1679       TCGA-64-1681       TCGA-64-5774       TCGA-64-5775 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-64-5778       TCGA-64-5779       TCGA-64-5781       TCGA-64-5815 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-67-3771       TCGA-67-3772       TCGA-67-3773       TCGA-67-4679 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-67-6215       TCGA-67-6216       TCGA-67-6217       TCGA-69-7760 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-69-7761       TCGA-69-7763       TCGA-69-7764       TCGA-69-7765 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-69-7973       TCGA-69-7974       TCGA-69-7978       TCGA-69-7979 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-69-7980       TCGA-69-8253       TCGA-69-8254       TCGA-69-8255 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-69-A59K       TCGA-71-6725       TCGA-71-8520       TCGA-73-4658 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4675       TCGA-73-4676       TCGA-73-4677 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-78-7143       TCGA-78-7145 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7146       TCGA-78-7147       TCGA-78-7148       TCGA-78-7149 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7150       TCGA-78-7152       TCGA-78-7153       TCGA-78-7154 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7155       TCGA-78-7156       TCGA-78-7158       TCGA-78-7159 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7160       TCGA-78-7161       TCGA-78-7162       TCGA-78-7163 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7167       TCGA-78-7220       TCGA-78-7535 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7536       TCGA-78-7539       TCGA-78-7540       TCGA-78-7542 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-78-7633       TCGA-83-5908       TCGA-86-6562       TCGA-86-6851 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-7953       TCGA-86-7954       TCGA-86-7955       TCGA-86-8054 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8073       TCGA-86-8074 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8075       TCGA-86-8076       TCGA-86-8278       TCGA-86-8279 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8280       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8585       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-8672       TCGA-86-8673       TCGA-86-8674       TCGA-86-A456 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-86-A4P8       TCGA-91-6828 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6830       TCGA-91-6831       TCGA-91-6835 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-91-6836       TCGA-91-6840       TCGA-91-6847       TCGA-91-6848 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-91-6849       TCGA-91-7771       TCGA-91-8496       TCGA-91-8497 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-91-8499       TCGA-91-A4BC       TCGA-91-A4BD       TCGA-93-7347 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-93-7348       TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-93-A4JP       TCGA-93-A4JQ       TCGA-95-7039       TCGA-95-7043 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-95-7567       TCGA-95-7944       TCGA-95-7947       TCGA-95-7948 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-95-8039       TCGA-95-8494       TCGA-95-A4VK       TCGA-95-A4VN 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-95-A4VP       TCGA-97-7546       TCGA-97-7547       TCGA-97-7552 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-97-7553       TCGA-97-7554       TCGA-97-7937       TCGA-97-7938 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-97-7941       TCGA-97-8171       TCGA-97-8172       TCGA-97-8175 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-97-8176       TCGA-97-8177       TCGA-97-8179       TCGA-97-8552 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-97-A4LX       TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M2 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-97-A4M3       TCGA-97-A4M5       TCGA-97-A4M6       TCGA-97-A4M7 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-99-8033       TCGA-J2-8192       TCGA-J2-8194       TCGA-J2-A4AD 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-J2-A4AE       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1       TCGA-MN-A4N4 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MN-A4N5       TCGA-MP-A4SW       TCGA-MP-A4SY       TCGA-MP-A4T2 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T9       TCGA-MP-A4TA 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MP-A4TC       TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A5C7       TCGA-NJ-A4YF 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-NJ-A4YP       TCGA-NJ-A4YQ 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
      TCGA-NJ-A55A       TCGA-NJ-A55O       TCGA-NJ-A55R       TCGA-O1-A52J 
"GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" "GTF2A1 WILD-TYPE" 
D127V15, binary
                  cls
clus                 0   1
  GTF2A1 MUTATED     0   2
  GTF2A1 WILD-TYPE   6 347
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2A1 MUTATED      0    2
  GTF2A1 WILD-TYPE    6  347
                        clus
vv                       GTF2A1 MUTATED GTF2A1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              2              347
[1] 2 2
[1] FALSE

Clustering(128) Variable = SERPINB13 MUTATION ANALYSIS
D128V1, survival
                     sevent
clus2                   0   1
  SERPINB13 MUTATED     8   1
  SERPINB13 WILD-TYPE 307 140
  SERPINB13 MUTATED SERPINB13 WILD-TYPE 
                  9                 447 
  SERPINB13 MUTATED SERPINB13 WILD-TYPE 
                  1                 140 
$`SERPINB13 MUTATED`
TCGA-05-4398 TCGA-05-4417 TCGA-38-4626 TCGA-44-6774 TCGA-44-7662 TCGA-50-5072 
       47.05        14.96       120.79        21.63         7.17         8.22 
TCGA-55-8089 TCGA-67-3771 TCGA-73-4668 
        3.29        20.05        15.35 

$`SERPINB13 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68        97.74        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SERPINB13 MUTATED SERPINB13 WILD-TYPE 
               3.29                0.00 
  SERPINB13 MUTATED SERPINB13 WILD-TYPE 
             120.79              223.96 
  SERPINB13 MUTATED SERPINB13 WILD-TYPE 
              15.35               18.08 
[1] "3.3 - 120.8 (15.3)" "0.0 - 224.0 (18.1)"
[1] "hr=" "3.7"
D128V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SERPINB13 MUTATED         0        2        3         1         1          2
  SERPINB13 WILD-TYPE       4      121      130        45        66         68
                     vv
clus                  STAGE IIIB STAGE IV
  SERPINB13 MUTATED            1        0
  SERPINB13 WILD-TYPE         10       25
D128V3, multiclass
            clus
vv           SERPINB13 MUTATED SERPINB13 WILD-TYPE
  STAGE I                    0                   4
  STAGE IA                   2                 121
  STAGE IB                   3                 130
  STAGE IIA                  1                  45
  STAGE IIB                  1                  66
  STAGE IIIA                 2                  68
  STAGE IIIB                 1                  10
  STAGE IV                   0                  25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  SERPINB13 MUTATED     3   6   0   1
  SERPINB13 WILD-TYPE 152 255  43  17
D128V4, multiclass
    clus
vv   SERPINB13 MUTATED SERPINB13 WILD-TYPE
  T1                 3                 152
  T2                 6                 255
  T3                 0                  43
  T4                 1                  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"
                     vv
clus                   N0  N1 N2+N3
  SERPINB13 MUTATED     6   1     3
  SERPINB13 WILD-TYPE 301  88    69
D128V5, multiclass
       clus
vv      SERPINB13 MUTATED SERPINB13 WILD-TYPE
  N0                    6                 301
  N1                    1                  88
  N2+N3                 3                  69
[1] 3 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
  SERPINB13 MUTATED     9   0
  SERPINB13 WILD-TYPE 318  23
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB13 MUTATED      9    0
  SERPINB13 WILD-TYPE  318   23
   clus
vv  SERPINB13 MUTATED SERPINB13 WILD-TYPE
  0                 9                 318
  1                 0                  23
[1] 2 2
[1] FALSE
D128V7, binary
                     cls
clus                    0   1
  SERPINB13 MUTATED     6   4
  SERPINB13 WILD-TYPE 253 217
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB13 MUTATED      6    4
  SERPINB13 WILD-TYPE  253  217
        clus
vv       SERPINB13 MUTATED SERPINB13 WILD-TYPE
  FEMALE                 6                 253
  MALE                   4                 217
[1] 2 2
[1] FALSE
D128V8, continuous
                     vv
clus                  LUNG ACINAR ADENOCARCINOMA
  SERPINB13 MUTATED                            0
  SERPINB13 WILD-TYPE                         18
                     vv
clus                  LUNG ADENOCARCINOMA MIXED SUBTYPE
  SERPINB13 MUTATED                                   2
  SERPINB13 WILD-TYPE                               100
                     vv
clus                  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SERPINB13 MUTATED                                                    7
  SERPINB13 WILD-TYPE                                                287
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SERPINB13 MUTATED                                            0
  SERPINB13 WILD-TYPE                                          4
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SERPINB13 MUTATED                                               0
  SERPINB13 WILD-TYPE                                            19
                     vv
clus                  LUNG CLEAR CELL ADENOCARCINOMA
  SERPINB13 MUTATED                                0
  SERPINB13 WILD-TYPE                              2
                     vv
clus                  LUNG MICROPAPILLARY ADENOCARCINOMA
  SERPINB13 MUTATED                                    1
  SERPINB13 WILD-TYPE                                  2
                     vv
clus                  LUNG MUCINOUS ADENOCARCINOMA
  SERPINB13 MUTATED                              0
  SERPINB13 WILD-TYPE                            2
                     vv
clus                  LUNG PAPILLARY ADENOCARCINOMA
  SERPINB13 MUTATED                               0
  SERPINB13 WILD-TYPE                            22
                     vv
clus                  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SERPINB13 MUTATED                                               0
  SERPINB13 WILD-TYPE                                             5
                     vv
clus                  MUCINOUS (COLLOID) CARCINOMA
  SERPINB13 MUTATED                              0
  SERPINB13 WILD-TYPE                            9
D128V9, multiclass
                                                    clus
vv                                                   SERPINB13 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                         0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      0
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       0
  LUNG PAPILLARY ADENOCARCINOMA                                      0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      0
  MUCINOUS (COLLOID) CARCINOMA                                       0
                                                    clus
vv                                                   SERPINB13 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                           4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                       19
  LUNG CLEAR CELL ADENOCARCINOMA                                       2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                   2
  LUNG MUCINOUS ADENOCARCINOMA                                         2
  LUNG PAPILLARY ADENOCARCINOMA                                       22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                        5
  MUCINOUS (COLLOID) CARCINOMA                                         9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V10, binary
                     cls
clus                    0   1
  SERPINB13 MUTATED     2   8
  SERPINB13 WILD-TYPE  18 452
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB13 MUTATED      2    8
  SERPINB13 WILD-TYPE   18  452
     clus
vv    SERPINB13 MUTATED SERPINB13 WILD-TYPE
  NO                  2                  18
  YES                 8                 452
[1] 2 2
[1] FALSE
D128V11, continuous
D128V12, continuous
                     vv
clus                   R0  R1  R2  RX
  SERPINB13 MUTATED     7   0   0   0
  SERPINB13 WILD-TYPE 303  11   4  25
D128V13, multiclass
    clus
vv   SERPINB13 MUTATED SERPINB13 WILD-TYPE
  R0                 7                 303
  R1                 0                  11
  R2                 0                   4
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINB13 MUTATED                                  1     0
  SERPINB13 WILD-TYPE                                0     7
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  SERPINB13 MUTATED                           1     5
  SERPINB13 WILD-TYPE                        28   372
D128V14, multiclass
                                  clus
vv                                 SERPINB13 MUTATED SERPINB13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 1                   0
  ASIAN                                            0                   7
  BLACK OR AFRICAN AMERICAN                        1                  28
  WHITE                                            5                 372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V15, binary
                     cls
clus                    0   1
  SERPINB13 MUTATED     0   7
  SERPINB13 WILD-TYPE   6 342
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB13 MUTATED      0    7
  SERPINB13 WILD-TYPE    6  342
                        clus
vv                       SERPINB13 MUTATED SERPINB13 WILD-TYPE
  HISPANIC OR LATINO                     0                   6
  NOT HISPANIC OR LATINO                 7                 342
[1] 2 2
[1] FALSE

Clustering(129) Variable = RAMP2 MUTATION ANALYSIS
D129V1, survival
                 sevent
clus2               0   1
  RAMP2 MUTATED     3   0
  RAMP2 WILD-TYPE 312 141
  RAMP2 MUTATED RAMP2 WILD-TYPE 
              3             453 
  RAMP2 MUTATED RAMP2 WILD-TYPE 
              0             141 
$`RAMP2 MUTATED`
TCGA-38-4626 TCGA-55-7907 TCGA-55-8089 
      120.79         0.53         3.29 

$`RAMP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  RAMP2 MUTATED RAMP2 WILD-TYPE 
           0.53            0.00 
  RAMP2 MUTATED RAMP2 WILD-TYPE 
         120.79          223.96 
  RAMP2 MUTATED RAMP2 WILD-TYPE 
           3.29           18.08 
[1] "0.5 - 120.8 (3.3)"  "0.0 - 224.0 (18.1)"
[1] "hr="     "9800000"
D129V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RAMP2 MUTATED         0        1        0         2         0          0
  RAMP2 WILD-TYPE       4      122      133        44        67         70
                 vv
clus              STAGE IIIB STAGE IV
  RAMP2 MUTATED            0        0
  RAMP2 WILD-TYPE         11       25
D129V3, multiclass
            clus
vv           RAMP2 MUTATED RAMP2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               0             133
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAMP2 MUTATED     1   2   0   0
  RAMP2 WILD-TYPE 154 259  43  18
D129V4, multiclass
    clus
vv   RAMP2 MUTATED RAMP2 WILD-TYPE
  T1             1             154
  T2             2             259
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  RAMP2 MUTATED     2   1     0
  RAMP2 WILD-TYPE 305  88    72
D129V5, multiclass
       clus
vv      RAMP2 MUTATED RAMP2 WILD-TYPE
  N0                2             305
  N1                1              88
  N2+N3             0              72
[1] 3 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
  RAMP2 MUTATED     2   0
  RAMP2 WILD-TYPE 325  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAMP2 MUTATED      2    0
  RAMP2 WILD-TYPE  325   23
   clus
vv  RAMP2 MUTATED RAMP2 WILD-TYPE
  0             2             325
  1             0              23
[1] 2 2
[1] FALSE
D129V7, binary
                 cls
clus                0   1
  RAMP2 MUTATED     1   2
  RAMP2 WILD-TYPE 258 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAMP2 MUTATED      1    2
  RAMP2 WILD-TYPE  258  219
        clus
vv       RAMP2 MUTATED RAMP2 WILD-TYPE
  FEMALE             1             258
  MALE               2             219
[1] 2 2
[1] FALSE
D129V8, continuous
[1] "Remove cluster labels:" "RAMP2 MUTATED"         
clus
  RAMP2 MUTATED RAMP2 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" "RAMP2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RAMP2 MUTATED                            0                                 0
  RAMP2 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RAMP2 MUTATED                                                    3
  RAMP2 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RAMP2 MUTATED                                            0
  RAMP2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RAMP2 MUTATED                                               0
  RAMP2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RAMP2 MUTATED                                0
  RAMP2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RAMP2 MUTATED                                    0
  RAMP2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RAMP2 MUTATED                              0                             0
  RAMP2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RAMP2 MUTATED                                               0
  RAMP2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RAMP2 MUTATED                              0
  RAMP2 WILD-TYPE                            9
D129V9, multiclass
                                                    clus
vv                                                   RAMP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   RAMP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V10, binary
                 cls
clus                0   1
  RAMP2 MUTATED     0   3
  RAMP2 WILD-TYPE  20 457
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAMP2 MUTATED      0    3
  RAMP2 WILD-TYPE   20  457
     clus
vv    RAMP2 MUTATED RAMP2 WILD-TYPE
  NO              0              20
  YES             3             457
[1] 2 2
[1] FALSE
D129V11, continuous
D129V12, continuous
                 vv
clus               R0  R1  R2  RX
  RAMP2 MUTATED     3   0   0   0
  RAMP2 WILD-TYPE 307  11   4  25
D129V13, multiclass
    clus
vv   RAMP2 MUTATED RAMP2 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAMP2 MUTATED                                  0     0
  RAMP2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAMP2 MUTATED                           0     3
  RAMP2 WILD-TYPE                        29   374
D129V14, multiclass
                                  clus
vv                                 RAMP2 MUTATED RAMP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        3             374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V15, binary
                 cls
clus                0   1
  RAMP2 MUTATED     0   3
  RAMP2 WILD-TYPE   6 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAMP2 MUTATED      0    3
  RAMP2 WILD-TYPE    6  346
                        clus
vv                       RAMP2 MUTATED RAMP2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             346
[1] 2 2
[1] FALSE

Clustering(130) Variable = RNASEH1 MUTATION ANALYSIS
D130V1, survival
                   sevent
clus2                 0   1
  RNASEH1 MUTATED     3   3
  RNASEH1 WILD-TYPE 312 138
  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
                6               450 
  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
                3               138 
$`RNASEH1 MUTATED`
TCGA-05-4427 TCGA-49-6761 TCGA-86-7711 TCGA-86-8073 TCGA-MP-A4T8 TCGA-MP-A4TA 
       26.01        11.64        34.39        24.33         5.29        31.23 

$`RNASEH1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
             5.29              0.00 
  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
            34.39            223.96 
  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
            25.17             17.95 
[1] "5.3 - 34.4 (25.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.9"
D130V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RNASEH1 MUTATED         0        1        1         1         1          2
  RNASEH1 WILD-TYPE       4      122      132        45        66         68
                   vv
clus                STAGE IIIB STAGE IV
  RNASEH1 MUTATED            0        0
  RNASEH1 WILD-TYPE         11       25
D130V3, multiclass
            clus
vv           RNASEH1 MUTATED RNASEH1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 1               132
  STAGE IIA                1                45
  STAGE IIB                1                66
  STAGE IIIA               2                68
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RNASEH1 MUTATED     2   4   0   0
  RNASEH1 WILD-TYPE 153 257  43  18
D130V4, multiclass
    clus
vv   RNASEH1 MUTATED RNASEH1 WILD-TYPE
  T1               2               153
  T2               4               257
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  RNASEH1 MUTATED     2   2     2
  RNASEH1 WILD-TYPE 305  87    70
D130V5, multiclass
       clus
vv      RNASEH1 MUTATED RNASEH1 WILD-TYPE
  N0                  2               305
  N1                  2                87
  N2+N3               2                70
[1] 3 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
  RNASEH1 MUTATED     5   0
  RNASEH1 WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RNASEH1 MUTATED      5    0
  RNASEH1 WILD-TYPE  322   23
   clus
vv  RNASEH1 MUTATED RNASEH1 WILD-TYPE
  0               5               322
  1               0                23
[1] 2 2
[1] FALSE
D130V7, binary
                   cls
clus                  0   1
  RNASEH1 MUTATED     3   3
  RNASEH1 WILD-TYPE 256 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RNASEH1 MUTATED      3    3
  RNASEH1 WILD-TYPE  256  218
        clus
vv       RNASEH1 MUTATED RNASEH1 WILD-TYPE
  FEMALE               3               256
  MALE                 3               218
[1] 2 2
[1] FALSE
D130V8, continuous
[1] "Remove cluster labels:" "RNASEH1 MUTATED"       
clus
  RNASEH1 MUTATED RNASEH1 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7713 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" "RNASEH1 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  RNASEH1 MUTATED                            0
  RNASEH1 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  RNASEH1 MUTATED                                   1
  RNASEH1 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RNASEH1 MUTATED                                                    4
  RNASEH1 WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RNASEH1 MUTATED                                            0
  RNASEH1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RNASEH1 MUTATED                                               1
  RNASEH1 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  RNASEH1 MUTATED                                0
  RNASEH1 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  RNASEH1 MUTATED                                    0
  RNASEH1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RNASEH1 MUTATED                              0                             0
  RNASEH1 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RNASEH1 MUTATED                                               0
  RNASEH1 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  RNASEH1 MUTATED                              0
  RNASEH1 WILD-TYPE                            9
D130V9, multiclass
                                                    clus
vv                                                   RNASEH1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   RNASEH1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V10, binary
                   cls
clus                  0   1
  RNASEH1 MUTATED     0   6
  RNASEH1 WILD-TYPE  20 454
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RNASEH1 MUTATED      0    6
  RNASEH1 WILD-TYPE   20  454
     clus
vv    RNASEH1 MUTATED RNASEH1 WILD-TYPE
  NO                0                20
  YES               6               454
[1] 2 2
[1] FALSE
D130V11, continuous
D130V12, continuous
                   vv
clus                 R0  R1  R2  RX
  RNASEH1 MUTATED     6   0   0   0
  RNASEH1 WILD-TYPE 304  11   4  25
D130V13, multiclass
    clus
vv   RNASEH1 MUTATED RNASEH1 WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNASEH1 MUTATED                                  0     0
  RNASEH1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RNASEH1 MUTATED                           0     4
  RNASEH1 WILD-TYPE                        29   373
D130V14, multiclass
                                  clus
vv                                 RNASEH1 MUTATED RNASEH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          4               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V15, binary
                   cls
clus                  0   1
  RNASEH1 MUTATED     1   3
  RNASEH1 WILD-TYPE   5 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RNASEH1 MUTATED      1    3
  RNASEH1 WILD-TYPE    5  346
                        clus
vv                       RNASEH1 MUTATED RNASEH1 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               3               346
[1] 2 2
[1] FALSE

Clustering(131) Variable = GLTSCR1 MUTATION ANALYSIS
D131V1, survival
                   sevent
clus2                 0   1
  GLTSCR1 MUTATED     6   2
  GLTSCR1 WILD-TYPE 309 139
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                8               448 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                2               139 
$`GLTSCR1 MUTATED`
TCGA-44-8117 TCGA-55-8616 TCGA-78-7148 TCGA-83-5908 TCGA-86-7701 TCGA-91-6829 
       12.66         1.58        20.58        27.09        31.13        41.36 
TCGA-95-7043 TCGA-97-7937 
        1.22         5.95 

$`GLTSCR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        10.55       110.50        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.12         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       25.48         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
             1.22              0.00 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
            41.36            223.96 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
            16.62             18.03 
[1] "1.2 - 41.4 (16.6)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D131V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GLTSCR1 MUTATED         0        2        4         0         1          0
  GLTSCR1 WILD-TYPE       4      121      129        46        66         70
                   vv
clus                STAGE IIIB STAGE IV
  GLTSCR1 MUTATED            0        1
  GLTSCR1 WILD-TYPE         11       24
D131V3, multiclass
            clus
vv           GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 4               129
  STAGE IIA                0                46
  STAGE IIB                1                66
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GLTSCR1 MUTATED     2   6   0   0
  GLTSCR1 WILD-TYPE 153 255  43  18
D131V4, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  T1               2               153
  T2               6               255
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  GLTSCR1 MUTATED     7   1     0
  GLTSCR1 WILD-TYPE 300  88    72
D131V5, multiclass
       clus
vv      GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  N0                  7               300
  N1                  1                88
  N2+N3               0                72
[1] 3 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
  GLTSCR1 MUTATED     4   1
  GLTSCR1 WILD-TYPE 323  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      4    1
  GLTSCR1 WILD-TYPE  323   22
   clus
vv  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  0               4               323
  1               1                22
[1] 2 2
[1] FALSE
D131V7, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     4   4
  GLTSCR1 WILD-TYPE 255 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      4    4
  GLTSCR1 WILD-TYPE  255  217
        clus
vv       GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  FEMALE               4               255
  MALE                 4               217
[1] 2 2
[1] FALSE
D131V8, continuous
[1] "Remove cluster labels:" "GLTSCR1 MUTATED"       
clus
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-75-5122        TCGA-86-7711        TCGA-86-7713        TCGA-86-7714 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-86-7954        TCGA-86-7955        TCGA-86-8055        TCGA-86-8056 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-86-8074        TCGA-86-8075        TCGA-86-8076        TCGA-86-8278 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8281        TCGA-86-8358        TCGA-86-8359 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-86-8668        TCGA-86-8669        TCGA-86-8671        TCGA-86-A4JF 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"GLTSCR1 WILD-TYPE" "GLTSCR1 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  GLTSCR1 MUTATED                            0
  GLTSCR1 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  GLTSCR1 MUTATED                                   2
  GLTSCR1 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GLTSCR1 MUTATED                                                    4
  GLTSCR1 WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GLTSCR1 MUTATED                                            0
  GLTSCR1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GLTSCR1 MUTATED                                               1
  GLTSCR1 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  GLTSCR1 MUTATED                                0
  GLTSCR1 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  GLTSCR1 MUTATED                                    1
  GLTSCR1 WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GLTSCR1 MUTATED                              0                             0
  GLTSCR1 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GLTSCR1 MUTATED                                               0
  GLTSCR1 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  GLTSCR1 MUTATED                              0
  GLTSCR1 WILD-TYPE                            9
D131V9, multiclass
                                                    clus
vv                                                   GLTSCR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   GLTSCR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V10, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     0   8
  GLTSCR1 WILD-TYPE  20 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      0    8
  GLTSCR1 WILD-TYPE   20  452
     clus
vv    GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  NO                0                20
  YES               8               452
[1] 2 2
[1] FALSE
D131V11, continuous
D131V12, continuous
                   vv
clus                 R0  R1  R2  RX
  GLTSCR1 MUTATED     5   0   0   0
  GLTSCR1 WILD-TYPE 305  11   4  25
D131V13, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  R0               5               305
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLTSCR1 MUTATED                                  0     0
  GLTSCR1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GLTSCR1 MUTATED                           0     8
  GLTSCR1 WILD-TYPE                        29   369
D131V14, multiclass
                                  clus
vv                                 GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          8               369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V15, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     0   7
  GLTSCR1 WILD-TYPE   6 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      0    7
  GLTSCR1 WILD-TYPE    6  342
                        clus
vv                       GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               7               342
[1] 2 2
[1] FALSE

Clustering(132) Variable = PDE1A MUTATION ANALYSIS
D132V1, survival
                 sevent
clus2               0   1
  PDE1A MUTATED    11   3
  PDE1A WILD-TYPE 304 138
  PDE1A MUTATED PDE1A WILD-TYPE 
             14             442 
  PDE1A MUTATED PDE1A WILD-TYPE 
              3             138 
$`PDE1A MUTATED`
TCGA-05-4430 TCGA-44-2657 TCGA-44-7670 TCGA-49-4505 TCGA-49-6743 TCGA-50-5930 
       25.02        13.15        29.00        14.07        12.13         9.27 
TCGA-53-7813 TCGA-55-8203 TCGA-55-8302 TCGA-64-5781 TCGA-78-7220 TCGA-86-6851 
       13.94        17.98         0.76        51.25        26.53         5.88 
TCGA-95-A4VK TCGA-97-7937 
       21.40         5.95 

$`PDE1A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        46.98        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       14.63        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        8.22        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       30.54         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       25.48         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  PDE1A MUTATED PDE1A WILD-TYPE 
           0.76            0.00 
  PDE1A MUTATED PDE1A WILD-TYPE 
          51.25          223.96 
  PDE1A MUTATED PDE1A WILD-TYPE 
         14.005          18.150 
[1] "0.8 - 51.2 (14.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D132V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PDE1A MUTATED         0        1        6         2         1          4
  PDE1A WILD-TYPE       4      122      127        44        66         66
                 vv
clus              STAGE IIIB STAGE IV
  PDE1A MUTATED            1        0
  PDE1A WILD-TYPE         10       25
D132V3, multiclass
            clus
vv           PDE1A MUTATED PDE1A WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               6             127
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             4              66
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDE1A MUTATED     5   9   0   1
  PDE1A WILD-TYPE 150 252  43  17
D132V4, multiclass
    clus
vv   PDE1A MUTATED PDE1A WILD-TYPE
  T1             5             150
  T2             9             252
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  PDE1A MUTATED     6   3     4
  PDE1A WILD-TYPE 301  86    68
D132V5, multiclass
       clus
vv      PDE1A MUTATED PDE1A WILD-TYPE
  N0                6             301
  N1                3              86
  N2+N3             4              68
[1] 3 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
  PDE1A MUTATED    11   0
  PDE1A WILD-TYPE 316  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED     11    0
  PDE1A WILD-TYPE  316   23
   clus
vv  PDE1A MUTATED PDE1A WILD-TYPE
  0            11             316
  1             0              23
[1] 2 2
[1] FALSE
D132V7, binary
                 cls
clus                0   1
  PDE1A MUTATED    11   4
  PDE1A WILD-TYPE 248 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED     11    4
  PDE1A WILD-TYPE  248  217
        clus
vv       PDE1A MUTATED PDE1A WILD-TYPE
  FEMALE            11             248
  MALE               4             217
[1] 2 2
[1] FALSE
D132V8, continuous
[1] "Remove cluster labels:" "PDE1A MUTATED"         
clus
  PDE1A MUTATED PDE1A WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8358 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"PDE1A WILD-TYPE" "PDE1A WILD-TYPE" "PDE1A WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PDE1A MUTATED                            0                                 6
  PDE1A WILD-TYPE                         18                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PDE1A MUTATED                                                    6
  PDE1A WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PDE1A MUTATED                                            0
  PDE1A WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PDE1A MUTATED                                               1
  PDE1A WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PDE1A MUTATED                                1
  PDE1A WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PDE1A MUTATED                                    1
  PDE1A WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PDE1A MUTATED                              0                             0
  PDE1A WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PDE1A MUTATED                                               0
  PDE1A WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PDE1A MUTATED                              0
  PDE1A WILD-TYPE                            9
D132V9, multiclass
                                                    clus
vv                                                   PDE1A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PDE1A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V10, binary
                 cls
clus                0   1
  PDE1A MUTATED     2  13
  PDE1A WILD-TYPE  18 447
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED      2   13
  PDE1A WILD-TYPE   18  447
     clus
vv    PDE1A MUTATED PDE1A WILD-TYPE
  NO              2              18
  YES            13             447
[1] 2 2
[1] FALSE
D132V11, continuous
D132V12, continuous
                 vv
clus               R0  R1  R2  RX
  PDE1A MUTATED     7   0   0   1
  PDE1A WILD-TYPE 303  11   4  24
D132V13, multiclass
    clus
vv   PDE1A MUTATED PDE1A WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDE1A MUTATED                                  0     0
  PDE1A WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDE1A MUTATED                           0    14
  PDE1A WILD-TYPE                        29   363
D132V14, multiclass
                                  clus
vv                                 PDE1A MUTATED PDE1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V15, binary
                 cls
clus                0   1
  PDE1A MUTATED     1  10
  PDE1A WILD-TYPE   5 339
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED      1   10
  PDE1A WILD-TYPE    5  339
                        clus
vv                       PDE1A MUTATED PDE1A WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            10             339
[1] 2 2
[1] FALSE

Clustering(133) Variable = SATB2 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  SATB2 MUTATED    21   8
  SATB2 WILD-TYPE 294 133
  SATB2 MUTATED SATB2 WILD-TYPE 
             29             427 
  SATB2 MUTATED SATB2 WILD-TYPE 
              8             133 
$`SATB2 MUTATED`
TCGA-05-4382 TCGA-05-4398 TCGA-05-4420 TCGA-38-4629 TCGA-44-3918 TCGA-44-6777 
       19.96        47.05        29.98        28.41        34.06        32.45 
TCGA-44-7672 TCGA-50-5045 TCGA-50-5066 TCGA-50-6594 TCGA-50-7109 TCGA-55-8511 
       23.64        71.47        31.04        12.16        10.13         0.30 
TCGA-55-A490 TCGA-64-1676 TCGA-64-5815 TCGA-69-7979 TCGA-73-4670 TCGA-78-7535 
        1.58        56.81        28.47         2.93         4.31        31.20 
TCGA-86-7955 TCGA-86-8358 TCGA-91-6836 TCGA-91-8499 TCGA-93-A4JN TCGA-97-7546 
       16.70        21.47        13.71         1.18        23.61        31.69 
TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A55A 
        3.81        38.63        14.10        19.13         0.26 

$`SATB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       63.72        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 
        7.17        36.07        18.87        29.00        17.59        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        22.26        20.52        70.55        15.72 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        51.25        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       13.87        20.55        19.43        19.89        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
        2.60        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
        6.12         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        18.18        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 
       35.47        16.44        19.00        14.30         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF 
       10.09        29.46        11.05        14.66        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64        29.13         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SATB2 MUTATED SATB2 WILD-TYPE 
           0.26            0.00 
  SATB2 MUTATED SATB2 WILD-TYPE 
          71.47          223.96 
  SATB2 MUTATED SATB2 WILD-TYPE 
          21.47           17.75 
[1] "0.3 - 71.5 (21.5)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D133V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SATB2 MUTATED         0        9       12         2         3          2
  SATB2 WILD-TYPE       4      114      121        44        64         68
                 vv
clus              STAGE IIIB STAGE IV
  SATB2 MUTATED            1        2
  SATB2 WILD-TYPE         10       23
D133V3, multiclass
            clus
vv           SATB2 MUTATED SATB2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               9             114
  STAGE IB              12             121
  STAGE IIA              2              44
  STAGE IIB              3              64
  STAGE IIIA             2              68
  STAGE IIIB             1              10
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SATB2 MUTATED     8  19   3   1
  SATB2 WILD-TYPE 147 242  40  17
D133V4, multiclass
    clus
vv   SATB2 MUTATED SATB2 WILD-TYPE
  T1             8             147
  T2            19             242
  T3             3              40
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  SATB2 MUTATED    23   4     3
  SATB2 WILD-TYPE 284  85    69
D133V5, multiclass
       clus
vv      SATB2 MUTATED SATB2 WILD-TYPE
  N0               23             284
  N1                4              85
  N2+N3             3              69
[1] 3 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
  SATB2 MUTATED    20   2
  SATB2 WILD-TYPE 307  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB2 MUTATED     20    2
  SATB2 WILD-TYPE  307   21
   clus
vv  SATB2 MUTATED SATB2 WILD-TYPE
  0            20             307
  1             2              21
[1] 2 2
[1] FALSE
D133V7, binary
                 cls
clus                0   1
  SATB2 MUTATED    16  15
  SATB2 WILD-TYPE 243 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB2 MUTATED     16   15
  SATB2 WILD-TYPE  243  206
        clus
vv       SATB2 MUTATED SATB2 WILD-TYPE
  FEMALE            16             243
  MALE              15             206
[1] 2 2
[1] FALSE
D133V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SATB2 MUTATED                            3                                 5
  SATB2 WILD-TYPE                         15                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SATB2 MUTATED                                                   21
  SATB2 WILD-TYPE                                                273
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SATB2 MUTATED                                            0
  SATB2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SATB2 MUTATED                                               0
  SATB2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SATB2 MUTATED                                0
  SATB2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SATB2 MUTATED                                    0
  SATB2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SATB2 MUTATED                              0                             1
  SATB2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SATB2 MUTATED                                               1
  SATB2 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SATB2 MUTATED                              0
  SATB2 WILD-TYPE                            9
D133V9, multiclass
                                                    clus
vv                                                   SATB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            21
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SATB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             273
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V10, binary
                 cls
clus                0   1
  SATB2 MUTATED     2  29
  SATB2 WILD-TYPE  18 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB2 MUTATED      2   29
  SATB2 WILD-TYPE   18  431
     clus
vv    SATB2 MUTATED SATB2 WILD-TYPE
  NO              2              18
  YES            29             431
[1] 2 2
[1] FALSE
D133V11, continuous
D133V12, continuous
                 vv
clus               R0  R1  R2  RX
  SATB2 MUTATED    19   0   1   2
  SATB2 WILD-TYPE 291  11   3  23
D133V13, multiclass
    clus
vv   SATB2 MUTATED SATB2 WILD-TYPE
  R0            19             291
  R1             0              11
  R2             1               3
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SATB2 MUTATED                                  0     0
  SATB2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SATB2 MUTATED                           3    22
  SATB2 WILD-TYPE                        26   355
D133V14, multiclass
                                  clus
vv                                 SATB2 MUTATED SATB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              26
  WHITE                                       22             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V15, binary
                 cls
clus                0   1
  SATB2 MUTATED     0  23
  SATB2 WILD-TYPE   6 326
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB2 MUTATED      0   23
  SATB2 WILD-TYPE    6  326
                        clus
vv                       SATB2 MUTATED SATB2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            23             326
[1] 2 2
[1] FALSE

Clustering(134) Variable = RAF1 MUTATION ANALYSIS
D134V1, survival
                sevent
clus2              0   1
  RAF1 MUTATED     5   1
  RAF1 WILD-TYPE 310 140
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            450 
  RAF1 MUTATED RAF1 WILD-TYPE 
             1            140 
$`RAF1 MUTATED`
TCGA-05-4427 TCGA-55-8505 TCGA-69-7765 TCGA-78-7220 TCGA-97-7546 TCGA-J2-8192 
       26.01         0.95         5.42        26.53        31.69        24.30 

$`RAF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      223.96         8.48        88.14        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       27.29         2.76        21.40        18.18        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85        36.76         1.45         5.59        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  RAF1 MUTATED RAF1 WILD-TYPE 
          0.95           0.00 
  RAF1 MUTATED RAF1 WILD-TYPE 
         31.69         223.96 
  RAF1 MUTATED RAF1 WILD-TYPE 
        25.155         17.950 
[1] "0.9 - 31.7 (25.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.4"
D134V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RAF1 MUTATED         0        1        0         1         1          2
  RAF1 WILD-TYPE       4      122      133        45        66         68
                vv
clus             STAGE IIIB STAGE IV
  RAF1 MUTATED            0        1
  RAF1 WILD-TYPE         11       24
D134V3, multiclass
            clus
vv           RAF1 MUTATED RAF1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              0            133
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAF1 MUTATED     2   3   0   1
  RAF1 WILD-TYPE 153 258  43  17
D134V4, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  T1            2            153
  T2            3            258
  T3            0             43
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  RAF1 MUTATED     2   2     2
  RAF1 WILD-TYPE 305  87    70
D134V5, multiclass
       clus
vv      RAF1 MUTATED RAF1 WILD-TYPE
  N0               2            305
  N1               2             87
  N2+N3            2             70
[1] 3 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
  RAF1 MUTATED     2   0
  RAF1 WILD-TYPE 325  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      2    0
  RAF1 WILD-TYPE  325   23
   clus
vv  RAF1 MUTATED RAF1 WILD-TYPE
  0            2            325
  1            0             23
[1] 2 2
[1] FALSE
D134V7, binary
                cls
clus               0   1
  RAF1 MUTATED     4   2
  RAF1 WILD-TYPE 255 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      4    2
  RAF1 WILD-TYPE  255  219
        clus
vv       RAF1 MUTATED RAF1 WILD-TYPE
  FEMALE            4            255
  MALE              2            219
[1] 2 2
[1] FALSE
D134V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RAF1 MUTATED                            1                                 3
  RAF1 WILD-TYPE                         17                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RAF1 MUTATED                                                    2
  RAF1 WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RAF1 MUTATED                                            0
  RAF1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RAF1 MUTATED                                               0
  RAF1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RAF1 MUTATED                                0
  RAF1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RAF1 MUTATED                                    0
  RAF1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RAF1 MUTATED                              0                             0
  RAF1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RAF1 MUTATED                                               0
  RAF1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RAF1 MUTATED                              0
  RAF1 WILD-TYPE                            9
D134V9, multiclass
                                                    clus
vv                                                   RAF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RAF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V10, binary
                cls
clus               0   1
  RAF1 MUTATED     1   5
  RAF1 WILD-TYPE  19 455
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      1    5
  RAF1 WILD-TYPE   19  455
     clus
vv    RAF1 MUTATED RAF1 WILD-TYPE
  NO             1             19
  YES            5            455
[1] 2 2
[1] FALSE
D134V11, continuous
D134V12, continuous
                vv
clus              R0  R1  R2  RX
  RAF1 MUTATED     4   0   0   0
  RAF1 WILD-TYPE 306  11   4  25
D134V13, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAF1 MUTATED                                  0     0
  RAF1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAF1 MUTATED                           1     4
  RAF1 WILD-TYPE                        28   373
D134V14, multiclass
                                  clus
vv                                 RAF1 MUTATED RAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       4            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V15, binary
                cls
clus               0   1
  RAF1 MUTATED     0   4
  RAF1 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      0    4
  RAF1 WILD-TYPE    6  345
                        clus
vv                       RAF1 MUTATED RAF1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(135) Variable = PLXND1 MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2                0   1
  PLXND1 MUTATED    12   2
  PLXND1 WILD-TYPE 303 139
  PLXND1 MUTATED PLXND1 WILD-TYPE 
              14              442 
  PLXND1 MUTATED PLXND1 WILD-TYPE 
               2              139 
$`PLXND1 MUTATED`
TCGA-05-4390 TCGA-44-2656 TCGA-50-6594 TCGA-50-7109 TCGA-55-7727 TCGA-55-8208 
       37.02        46.98        12.16        10.13         1.12        22.16 
TCGA-55-8620 TCGA-67-3771 TCGA-67-6215 TCGA-69-8255 TCGA-69-A59K TCGA-86-8073 
        2.17        20.05         5.72         4.24         7.04        24.33 
TCGA-NJ-A4YP TCGA-NJ-A4YQ 
        1.64        29.13 

$`PLXND1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
       11.05         6.21        41.69         0.72        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.28         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
        6.64        17.62         0.49         1.58         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       18.84        14.04         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-71-8520 
        2.93        12.56        14.01        13.45         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  PLXND1 MUTATED PLXND1 WILD-TYPE 
            1.12             0.00 
  PLXND1 MUTATED PLXND1 WILD-TYPE 
           46.98           223.96 
  PLXND1 MUTATED PLXND1 WILD-TYPE 
          11.145           18.100 
[1] "1.1 - 47.0 (11.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D135V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PLXND1 MUTATED         0        5        5         0         1          3
  PLXND1 WILD-TYPE       4      118      128        46        66         67
                  vv
clus               STAGE IIIB STAGE IV
  PLXND1 MUTATED            0        1
  PLXND1 WILD-TYPE         11       24
D135V3, multiclass
            clus
vv           PLXND1 MUTATED PLXND1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              118
  STAGE IB                5              128
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLXND1 MUTATED     7   5   3   0
  PLXND1 WILD-TYPE 148 256  40  18
D135V4, multiclass
    clus
vv   PLXND1 MUTATED PLXND1 WILD-TYPE
  T1              7              148
  T2              5              256
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  PLXND1 MUTATED    11   1     3
  PLXND1 WILD-TYPE 296  88    69
D135V5, multiclass
       clus
vv      PLXND1 MUTATED PLXND1 WILD-TYPE
  N0                11              296
  N1                 1               88
  N2+N3              3               69
[1] 3 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
  PLXND1 MUTATED    13   1
  PLXND1 WILD-TYPE 314  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXND1 MUTATED     13    1
  PLXND1 WILD-TYPE  314   22
   clus
vv  PLXND1 MUTATED PLXND1 WILD-TYPE
  0             13              314
  1              1               22
[1] 2 2
[1] FALSE
D135V7, binary
                  cls
clus                 0   1
  PLXND1 MUTATED     8   7
  PLXND1 WILD-TYPE 251 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXND1 MUTATED      8    7
  PLXND1 WILD-TYPE  251  214
        clus
vv       PLXND1 MUTATED PLXND1 WILD-TYPE
  FEMALE              8              251
  MALE                7              214
[1] 2 2
[1] FALSE
D135V8, continuous
[1] "Remove cluster labels:" "PLXND1 MUTATED"        
clus
  PLXND1 MUTATED PLXND1 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5778       TCGA-69-7974 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4676 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"PLXND1 WILD-TYPE" "PLXND1 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PLXND1 MUTATED                            0                                 2
  PLXND1 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PLXND1 MUTATED                                                    9
  PLXND1 WILD-TYPE                                                285
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PLXND1 MUTATED                                            0
  PLXND1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PLXND1 MUTATED                                               1
  PLXND1 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  PLXND1 MUTATED                                0
  PLXND1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  PLXND1 MUTATED                                    0
  PLXND1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PLXND1 MUTATED                              0                             2
  PLXND1 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PLXND1 MUTATED                                               1
  PLXND1 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  PLXND1 MUTATED                              0
  PLXND1 WILD-TYPE                            9
D135V9, multiclass
                                                    clus
vv                                                   PLXND1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   PLXND1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V10, binary
                  cls
clus                 0   1
  PLXND1 MUTATED     0  15
  PLXND1 WILD-TYPE  20 445
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXND1 MUTATED      0   15
  PLXND1 WILD-TYPE   20  445
     clus
vv    PLXND1 MUTATED PLXND1 WILD-TYPE
  NO               0               20
  YES             15              445
[1] 2 2
[1] FALSE
D135V11, continuous
D135V12, continuous
                  vv
clus                R0  R1  R2  RX
  PLXND1 MUTATED     7   0   1   1
  PLXND1 WILD-TYPE 303  11   3  24
D135V13, multiclass
    clus
vv   PLXND1 MUTATED PLXND1 WILD-TYPE
  R0              7              303
  R1              0               11
  R2              1                3
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLXND1 MUTATED                                  0     0
  PLXND1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PLXND1 MUTATED                           3    10
  PLXND1 WILD-TYPE                        26   367
D135V14, multiclass
                                  clus
vv                                 PLXND1 MUTATED PLXND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V15, binary
                  cls
clus                 0   1
  PLXND1 MUTATED     1  12
  PLXND1 WILD-TYPE   5 337
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXND1 MUTATED      1   12
  PLXND1 WILD-TYPE    5  337
                        clus
vv                       PLXND1 MUTATED PLXND1 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             12              337
[1] 2 2
[1] FALSE

Clustering(136) Variable = OFD1 MUTATION ANALYSIS
D136V1, survival
                sevent
clus2              0   1
  OFD1 MUTATED     9   5
  OFD1 WILD-TYPE 306 136
  OFD1 MUTATED OFD1 WILD-TYPE 
            14            442 
  OFD1 MUTATED OFD1 WILD-TYPE 
             5            136 
$`OFD1 MUTATED`
TCGA-05-4382 TCGA-44-A47A TCGA-55-7570 TCGA-55-A4DF TCGA-73-4659 TCGA-78-7150 
       19.96        15.32         0.20        20.19        23.38        21.90 
TCGA-86-6851 TCGA-86-7711 TCGA-97-A4M3 TCGA-99-8033 TCGA-L9-A444 TCGA-MP-A4TF 
        5.88        34.39        17.75         5.59         0.20        11.05 
TCGA-NJ-A4YG TCGA-NJ-A4YP 
       62.60         1.64 

$`OFD1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.98         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         1.15         7.99         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
       27.16         5.69        19.27        20.58        35.93        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 
      110.50        27.09        12.36        31.13        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 
       20.19        21.44        19.76        20.52        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 
       20.68        24.56        34.85        36.76         1.45        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH 
       41.59        31.23         2.43        10.09        29.46        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       14.10        19.13        73.91        71.05         0.13        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  OFD1 MUTATED OFD1 WILD-TYPE 
           0.2            0.0 
  OFD1 MUTATED OFD1 WILD-TYPE 
         62.60         223.96 
  OFD1 MUTATED OFD1 WILD-TYPE 
        16.535         18.100 
[1] "0.2 - 62.6 (16.5)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D136V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  OFD1 MUTATED         0        4        5         3         1          1
  OFD1 WILD-TYPE       4      119      128        43        66         69
                vv
clus             STAGE IIIB STAGE IV
  OFD1 MUTATED            0        1
  OFD1 WILD-TYPE         11       24
D136V3, multiclass
            clus
vv           OFD1 MUTATED OFD1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              5            128
  STAGE IIA             3             43
  STAGE IIB             1             66
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OFD1 MUTATED     5   9   0   0
  OFD1 WILD-TYPE 150 252  43  18
D136V4, multiclass
    clus
vv   OFD1 MUTATED OFD1 WILD-TYPE
  T1            5            150
  T2            9            252
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  OFD1 MUTATED    10   3     1
  OFD1 WILD-TYPE 297  86    71
D136V5, multiclass
       clus
vv      OFD1 MUTATED OFD1 WILD-TYPE
  N0              10            297
  N1               3             86
  N2+N3            1             71
[1] 3 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
  OFD1 MUTATED    10   1
  OFD1 WILD-TYPE 317  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED     10    1
  OFD1 WILD-TYPE  317   22
   clus
vv  OFD1 MUTATED OFD1 WILD-TYPE
  0           10            317
  1            1             22
[1] 2 2
[1] FALSE
D136V7, binary
                cls
clus               0   1
  OFD1 MUTATED     6   9
  OFD1 WILD-TYPE 253 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      6    9
  OFD1 WILD-TYPE  253  212
        clus
vv       OFD1 MUTATED OFD1 WILD-TYPE
  FEMALE            6            253
  MALE              9            212
[1] 2 2
[1] FALSE
D136V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  OFD1 MUTATED                            0                                 3
  OFD1 WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  OFD1 MUTATED                                                   11
  OFD1 WILD-TYPE                                                283
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  OFD1 MUTATED                                            0
  OFD1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  OFD1 MUTATED                                               0
  OFD1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  OFD1 MUTATED                                0
  OFD1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  OFD1 MUTATED                                    0
  OFD1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  OFD1 MUTATED                              0                             1
  OFD1 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  OFD1 MUTATED                                               0
  OFD1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  OFD1 MUTATED                              0
  OFD1 WILD-TYPE                            9
D136V9, multiclass
                                                    clus
vv                                                   OFD1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   OFD1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V10, binary
                cls
clus               0   1
  OFD1 MUTATED     0  15
  OFD1 WILD-TYPE  20 445
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      0   15
  OFD1 WILD-TYPE   20  445
     clus
vv    OFD1 MUTATED OFD1 WILD-TYPE
  NO             0             20
  YES           15            445
[1] 2 2
[1] FALSE
D136V11, continuous
D136V12, continuous
                vv
clus              R0  R1  R2  RX
  OFD1 MUTATED    11   0   0   0
  OFD1 WILD-TYPE 299  11   4  25
D136V13, multiclass
    clus
vv   OFD1 MUTATED OFD1 WILD-TYPE
  R0           11            299
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OFD1 MUTATED                                  0     0
  OFD1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OFD1 MUTATED                           1    12
  OFD1 WILD-TYPE                        28   365
D136V14, multiclass
                                  clus
vv                                 OFD1 MUTATED OFD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      12            365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V15, binary
                cls
clus               0   1
  OFD1 MUTATED     1  10
  OFD1 WILD-TYPE   5 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      1   10
  OFD1 WILD-TYPE    5  339
                        clus
vv                       OFD1 MUTATED OFD1 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(137) Variable = APLF MUTATION ANALYSIS
D137V1, survival
                sevent
clus2              0   1
  APLF MUTATED     3   1
  APLF WILD-TYPE 312 140
  APLF MUTATED APLF WILD-TYPE 
             4            452 
  APLF MUTATED APLF WILD-TYPE 
             1            140 
$`APLF MUTATED`
TCGA-05-4417 TCGA-62-A46R TCGA-91-6831 TCGA-97-7546 
       14.96        56.71        10.19        31.69 

$`APLF WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  APLF MUTATED APLF WILD-TYPE 
         10.19           0.00 
  APLF MUTATED APLF WILD-TYPE 
         56.71         223.96 
  APLF MUTATED APLF WILD-TYPE 
        23.325         18.030 
[1] "10.2 - 56.7 (23.3)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D137V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  APLF MUTATED         0        1        3         0         0          0
  APLF WILD-TYPE       4      122      130        46        67         70
                vv
clus             STAGE IIIB STAGE IV
  APLF MUTATED            0        0
  APLF WILD-TYPE         11       25
D137V3, multiclass
            clus
vv           APLF MUTATED APLF WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  APLF MUTATED     1   3   0   0
  APLF WILD-TYPE 154 258  43  18
D137V4, multiclass
    clus
vv   APLF MUTATED APLF WILD-TYPE
  T1            1            154
  T2            3            258
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  APLF MUTATED     4   0     0
  APLF WILD-TYPE 303  89    72
D137V5, multiclass
       clus
vv      APLF MUTATED APLF WILD-TYPE
  N0               4            303
  N1               0             89
  N2+N3            0             72
[1] 3 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
  APLF MUTATED     2   0
  APLF WILD-TYPE 325  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  APLF MUTATED      2    0
  APLF WILD-TYPE  325   23
   clus
vv  APLF MUTATED APLF WILD-TYPE
  0            2            325
  1            0             23
[1] 2 2
[1] FALSE
D137V7, binary
                cls
clus               0   1
  APLF MUTATED     3   1
  APLF WILD-TYPE 256 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  APLF MUTATED      3    1
  APLF WILD-TYPE  256  220
        clus
vv       APLF MUTATED APLF WILD-TYPE
  FEMALE            3            256
  MALE              1            220
[1] 2 2
[1] FALSE
D137V8, continuous
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46S     TCGA-62-A46U 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  APLF MUTATED                            1                                 2
  APLF WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  APLF MUTATED                                                    1
  APLF WILD-TYPE                                                293
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  APLF MUTATED                                            0
  APLF WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  APLF MUTATED                                               0
  APLF WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  APLF MUTATED                                0
  APLF WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  APLF MUTATED                                    0
  APLF WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  APLF MUTATED                              0                             0
  APLF WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  APLF MUTATED                                               0
  APLF WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  APLF MUTATED                              0
  APLF WILD-TYPE                            9
D137V9, multiclass
                                                    clus
vv                                                   APLF MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   APLF WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V10, binary
                cls
clus               0   1
  APLF MUTATED     0   4
  APLF WILD-TYPE  20 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  APLF MUTATED      0    4
  APLF WILD-TYPE   20  456
     clus
vv    APLF MUTATED APLF WILD-TYPE
  NO             0             20
  YES            4            456
[1] 2 2
[1] FALSE
D137V11, continuous
D137V12, continuous
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4424     TCGA-05-4427 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-05-4433     TCGA-05-5420     TCGA-05-5423     TCGA-05-5425 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-05-5428     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-7271     TCGA-38-A44F 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-3396     TCGA-44-3398 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-5644     TCGA-44-5645 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6147     TCGA-44-6148 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4494     TCGA-49-4505     TCGA-53-7624 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-1592 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-1595     TCGA-55-5899     TCGA-55-6642     TCGA-55-6712 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-6971     TCGA-55-7227     TCGA-55-7283     TCGA-55-7570 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7728     TCGA-55-7907     TCGA-55-7910 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7914     TCGA-55-8089     TCGA-55-8092 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8205 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8506 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8511     TCGA-55-8512     TCGA-55-8514 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-62-8398 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5774     TCGA-64-5775 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5779     TCGA-64-5781     TCGA-69-7761 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-69-7763     TCGA-69-7764     TCGA-69-7765     TCGA-69-7974 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-69-7979     TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-7498 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7031 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-7145     TCGA-78-7146     TCGA-78-7147     TCGA-78-7148 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-7149     TCGA-78-7150     TCGA-78-7152     TCGA-78-7153 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-7154     TCGA-78-7155     TCGA-78-7156     TCGA-78-7158 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-7159     TCGA-78-7160     TCGA-78-7161     TCGA-78-7162 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-7163     TCGA-78-7166     TCGA-78-7167     TCGA-78-7220 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-7535     TCGA-78-7536     TCGA-78-7537     TCGA-78-7539 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-80-5608     TCGA-83-5908     TCGA-86-6851     TCGA-86-7711 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-8054     TCGA-86-8055 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8281 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8669     TCGA-86-8673 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-91-6829     TCGA-91-6830 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-91-6836     TCGA-91-6840     TCGA-91-6849     TCGA-91-8499 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-91-A4BC     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7567     TCGA-95-7944     TCGA-95-7947 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-95-7948     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  APLF MUTATED     3   0   0   0
  APLF WILD-TYPE 307  11   4  25
D137V13, multiclass
    clus
vv   APLF MUTATED APLF WILD-TYPE
  R0            3            307
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APLF MUTATED                                  0     0
  APLF WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  APLF MUTATED                           0     3
  APLF WILD-TYPE                        29   374
D137V14, multiclass
                                  clus
vv                                 APLF MUTATED APLF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       3            374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V15, binary
                cls
clus               0   1
  APLF MUTATED     0   3
  APLF WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  APLF MUTATED      0    3
  APLF WILD-TYPE    6  346
                        clus
vv                       APLF MUTATED APLF WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(138) Variable = ADAMTS2 MUTATION ANALYSIS
D138V1, survival
                   sevent
clus2                 0   1
  ADAMTS2 MUTATED    30   7
  ADAMTS2 WILD-TYPE 285 134
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               37               419 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
                7               134 
$`ADAMTS2 MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4427 TCGA-44-4112 
       19.96        37.02         0.00        24.03        26.01        26.56 
TCGA-44-6777 TCGA-44-A47F TCGA-50-6593 TCGA-55-6642 TCGA-55-7227 TCGA-55-7281 
       32.45        11.08        11.05        32.65         1.74         0.59 
TCGA-55-7995 TCGA-55-8089 TCGA-55-8207 TCGA-55-8506 TCGA-55-8616 TCGA-55-A492 
        0.16         3.29         2.17         0.36         1.58        19.59 
TCGA-55-A4DG TCGA-64-1676 TCGA-69-7980 TCGA-78-7155 TCGA-83-5908 TCGA-86-7713 
       19.99        56.81        12.56        38.50        27.09        13.87 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-A456 TCGA-91-6831 TCGA-93-8067 
       16.70         4.57        24.33        13.32        10.19         6.12 
TCGA-95-7039 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A444 TCGA-NJ-A4YF TCGA-NJ-A4YI 
        1.12        17.75        23.80         0.20        71.05         0.13 
TCGA-NJ-A4YQ 
       29.13 

$`ADAMTS2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
       50.07         3.98        14.01        45.01         9.96        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
        8.02        19.00        20.05         2.99        14.96         9.01 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       22.03         9.04         2.04         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        6.25        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       40.54       107.21        70.26         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
        0.10         4.80         6.64        17.62         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       20.58         0.92        15.81        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30         2.93        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55       110.50        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       34.39        20.55        19.43        19.89        24.49         4.08 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        14.96        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36         1.97         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
        1.18         1.45        19.82         9.76         4.18        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 
       20.58        20.19        21.44        19.76        20.52        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG 
       11.05        14.66        14.10        19.13        73.91        62.60 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64         0.26         0.43        19.82        59.11 

  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
             0.00              0.07 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
            71.05            223.96 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
            13.87             18.18 
[1] "0.0 - 71.0 (13.9)"  "0.1 - 224.0 (18.2)"
[1] "hr=" "1.2"
D138V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADAMTS2 MUTATED         1       13       13         1         6          4
  ADAMTS2 WILD-TYPE       3      110      120        45        61         66
                   vv
clus                STAGE IIIB STAGE IV
  ADAMTS2 MUTATED            1        0
  ADAMTS2 WILD-TYPE         10       25
D138V3, multiclass
            clus
vv           ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                13               110
  STAGE IB                13               120
  STAGE IIA                1                45
  STAGE IIB                6                61
  STAGE IIIA               4                66
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ADAMTS2 MUTATED    15  18   4   2
  ADAMTS2 WILD-TYPE 140 243  39  16
D138V4, multiclass
    clus
vv   ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  T1              15               140
  T2              18               243
  T3               4                39
  T4               2                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"
                   vv
clus                 N0  N1 N2+N3
  ADAMTS2 MUTATED    31   4     3
  ADAMTS2 WILD-TYPE 276  85    69
D138V5, multiclass
       clus
vv      ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  N0                 31               276
  N1                  4                85
  N2+N3               3                69
[1] 3 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
  ADAMTS2 MUTATED    27   0
  ADAMTS2 WILD-TYPE 300  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED     27    0
  ADAMTS2 WILD-TYPE  300   23
   clus
vv  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  0              27               300
  1               0                23
[1] 2 2
[1] FALSE
D138V7, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED    22  17
  ADAMTS2 WILD-TYPE 237 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED     22   17
  ADAMTS2 WILD-TYPE  237  204
        clus
vv       ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  FEMALE              22               237
  MALE                17               204
[1] 2 2
[1] FALSE
D138V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ADAMTS2 MUTATED                            1
  ADAMTS2 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADAMTS2 MUTATED                                  11
  ADAMTS2 WILD-TYPE                                91
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADAMTS2 MUTATED                                                   24
  ADAMTS2 WILD-TYPE                                                270
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADAMTS2 MUTATED                                            0
  ADAMTS2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADAMTS2 MUTATED                                               1
  ADAMTS2 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ADAMTS2 MUTATED                                0
  ADAMTS2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ADAMTS2 MUTATED                                    0
  ADAMTS2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADAMTS2 MUTATED                              0                             2
  ADAMTS2 WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADAMTS2 MUTATED                                               0
  ADAMTS2 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ADAMTS2 MUTATED                              0
  ADAMTS2 WILD-TYPE                            9
D138V9, multiclass
                                                    clus
vv                                                   ADAMTS2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              24
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ADAMTS2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V10, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED     1  38
  ADAMTS2 WILD-TYPE  19 422
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED      1   38
  ADAMTS2 WILD-TYPE   19  422
     clus
vv    ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  NO                1                19
  YES              38               422
[1] 2 2
[1] FALSE
D138V11, continuous
D138V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ADAMTS2 MUTATED    26   0   0   3
  ADAMTS2 WILD-TYPE 284  11   4  22
D138V13, multiclass
    clus
vv   ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  R0              26               284
  R1               0                11
  R2               0                 4
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS2 MUTATED                                  0     2
  ADAMTS2 WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS2 MUTATED                           1    29
  ADAMTS2 WILD-TYPE                        28   348
D138V14, multiclass
                                  clus
vv                                 ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                         29               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V15, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED     0  27
  ADAMTS2 WILD-TYPE   6 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED      0   27
  ADAMTS2 WILD-TYPE    6  322
                        clus
vv                       ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              27               322
[1] 2 2
[1] FALSE

Clustering(139) Variable = CAPN11 MUTATION ANALYSIS
D139V1, survival
                  sevent
clus2                0   1
  CAPN11 MUTATED     8   4
  CAPN11 WILD-TYPE 307 137
  CAPN11 MUTATED CAPN11 WILD-TYPE 
              12              444 
  CAPN11 MUTATED CAPN11 WILD-TYPE 
               4              137 
$`CAPN11 MUTATED`
TCGA-05-4250 TCGA-05-4427 TCGA-35-5375 TCGA-44-4112 TCGA-50-6590 TCGA-55-1592 
        3.98        26.01         8.68        26.56        42.35        23.05 
TCGA-64-5781 TCGA-67-3771 TCGA-69-7979 TCGA-86-6851 TCGA-86-8358 TCGA-MN-A4N4 
       51.25        20.05         2.93         5.88        21.47        38.63 

$`CAPN11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24        34.06         6.25        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 
       34.29        30.54        13.94         9.21        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       38.37        87.98         2.04        42.90        28.41        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  CAPN11 MUTATED CAPN11 WILD-TYPE 
            2.93             0.00 
  CAPN11 MUTATED CAPN11 WILD-TYPE 
           51.25           223.96 
  CAPN11 MUTATED CAPN11 WILD-TYPE 
          22.260           17.835 
[1] "2.9 - 51.2 (22.3)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D139V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CAPN11 MUTATED         0        3        5         1         1          2
  CAPN11 WILD-TYPE       4      120      128        45        66         68
                  vv
clus               STAGE IIIB STAGE IV
  CAPN11 MUTATED            0        0
  CAPN11 WILD-TYPE         11       25
D139V3, multiclass
            clus
vv           CAPN11 MUTATED CAPN11 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                5              128
  STAGE IIA               1               45
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CAPN11 MUTATED     3   8   1   0
  CAPN11 WILD-TYPE 152 253  42  18
D139V4, multiclass
    clus
vv   CAPN11 MUTATED CAPN11 WILD-TYPE
  T1              3              152
  T2              8              253
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  CAPN11 MUTATED     8   3     1
  CAPN11 WILD-TYPE 299  86    71
D139V5, multiclass
       clus
vv      CAPN11 MUTATED CAPN11 WILD-TYPE
  N0                 8              299
  N1                 3               86
  N2+N3              1               71
[1] 3 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
  CAPN11 MUTATED    11   0
  CAPN11 WILD-TYPE 316  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPN11 MUTATED     11    0
  CAPN11 WILD-TYPE  316   23
   clus
vv  CAPN11 MUTATED CAPN11 WILD-TYPE
  0             11              316
  1              0               23
[1] 2 2
[1] FALSE
D139V7, binary
                  cls
clus                 0   1
  CAPN11 MUTATED     8   4
  CAPN11 WILD-TYPE 251 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPN11 MUTATED      8    4
  CAPN11 WILD-TYPE  251  217
        clus
vv       CAPN11 MUTATED CAPN11 WILD-TYPE
  FEMALE              8              251
  MALE                4              217
[1] 2 2
[1] FALSE
D139V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CAPN11 MUTATED                            1                                 3
  CAPN11 WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CAPN11 MUTATED                                                    8
  CAPN11 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CAPN11 MUTATED                                            0
  CAPN11 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CAPN11 MUTATED                                               0
  CAPN11 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CAPN11 MUTATED                                0
  CAPN11 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CAPN11 MUTATED                                    0
  CAPN11 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CAPN11 MUTATED                              0                             0
  CAPN11 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CAPN11 MUTATED                                               0
  CAPN11 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CAPN11 MUTATED                              0
  CAPN11 WILD-TYPE                            9
D139V9, multiclass
                                                    clus
vv                                                   CAPN11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CAPN11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V10, binary
                  cls
clus                 0   1
  CAPN11 MUTATED     0  12
  CAPN11 WILD-TYPE  20 448
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPN11 MUTATED      0   12
  CAPN11 WILD-TYPE   20  448
     clus
vv    CAPN11 MUTATED CAPN11 WILD-TYPE
  NO               0               20
  YES             12              448
[1] 2 2
[1] FALSE
D139V11, continuous
D139V12, continuous
                  vv
clus                R0  R1  R2  RX
  CAPN11 MUTATED     8   0   1   0
  CAPN11 WILD-TYPE 302  11   3  25
D139V13, multiclass
    clus
vv   CAPN11 MUTATED CAPN11 WILD-TYPE
  R0              8              302
  R1              0               11
  R2              1                3
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPN11 MUTATED                                  0     0
  CAPN11 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CAPN11 MUTATED                           1     9
  CAPN11 WILD-TYPE                        28   368
D139V14, multiclass
                                  clus
vv                                 CAPN11 MUTATED CAPN11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V15, binary
                  cls
clus                 0   1
  CAPN11 MUTATED     0  10
  CAPN11 WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPN11 MUTATED      0   10
  CAPN11 WILD-TYPE    6  339
                        clus
vv                       CAPN11 MUTATED CAPN11 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(140) Variable = FLCN MUTATION ANALYSIS
D140V1, survival
                sevent
clus2              0   1
  FLCN MUTATED     5   5
  FLCN WILD-TYPE 310 136
  FLCN MUTATED FLCN WILD-TYPE 
            10            446 
  FLCN MUTATED FLCN WILD-TYPE 
             5            136 
$`FLCN MUTATED`
TCGA-05-4397 TCGA-53-7626 TCGA-55-7281 TCGA-55-8511 TCGA-55-8615 TCGA-62-A46O 
       24.03        30.54         0.59         0.30         0.49        47.80 
TCGA-78-7154 TCGA-78-7537 TCGA-93-A4JN TCGA-97-8175 
       19.50        53.33        23.61        18.12 

$`FLCN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        25.61         7.59        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80         6.64        17.62         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
       31.20         8.02        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        9.76         4.18         6.12         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 
        0.59         0.72        18.67        17.92         5.39        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  FLCN MUTATED FLCN WILD-TYPE 
           0.3            0.0 
  FLCN MUTATED FLCN WILD-TYPE 
         53.33         223.96 
  FLCN MUTATED FLCN WILD-TYPE 
        21.555         17.835 
[1] "0.3 - 53.3 (21.6)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.7"
D140V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FLCN MUTATED         0        1        4         1         1          2
  FLCN WILD-TYPE       4      122      129        45        66         68
                vv
clus             STAGE IIIB STAGE IV
  FLCN MUTATED            0        1
  FLCN WILD-TYPE         11       24
D140V3, multiclass
            clus
vv           FLCN MUTATED FLCN WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              4            129
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLCN MUTATED     2   6   2   0
  FLCN WILD-TYPE 153 255  41  18
D140V4, multiclass
    clus
vv   FLCN MUTATED FLCN WILD-TYPE
  T1            2            153
  T2            6            255
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  FLCN MUTATED     6   2     2
  FLCN WILD-TYPE 301  87    70
D140V5, multiclass
       clus
vv      FLCN MUTATED FLCN WILD-TYPE
  N0               6            301
  N1               2             87
  N2+N3            2             70
[1] 3 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
  FLCN MUTATED     7   1
  FLCN WILD-TYPE 320  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      7    1
  FLCN WILD-TYPE  320   22
   clus
vv  FLCN MUTATED FLCN WILD-TYPE
  0            7            320
  1            1             22
[1] 2 2
[1] FALSE
D140V7, binary
                cls
clus               0   1
  FLCN MUTATED     5   5
  FLCN WILD-TYPE 254 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      5    5
  FLCN WILD-TYPE  254  216
        clus
vv       FLCN MUTATED FLCN WILD-TYPE
  FEMALE            5            254
  MALE              5            216
[1] 2 2
[1] FALSE
D140V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FLCN MUTATED                            1                                 2
  FLCN WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FLCN MUTATED                                                    6
  FLCN WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FLCN MUTATED                                            0
  FLCN WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FLCN MUTATED                                               0
  FLCN WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  FLCN MUTATED                                0
  FLCN WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  FLCN MUTATED                                    0
  FLCN WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FLCN MUTATED                              0                             0
  FLCN WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FLCN MUTATED                                               1
  FLCN WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  FLCN MUTATED                              0
  FLCN WILD-TYPE                            9
D140V9, multiclass
                                                    clus
vv                                                   FLCN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   FLCN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V10, binary
                cls
clus               0   1
  FLCN MUTATED     0  10
  FLCN WILD-TYPE  20 450
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      0   10
  FLCN WILD-TYPE   20  450
     clus
vv    FLCN MUTATED FLCN WILD-TYPE
  NO             0             20
  YES           10            450
[1] 2 2
[1] FALSE
D140V11, continuous
D140V12, continuous
                vv
clus              R0  R1  R2  RX
  FLCN MUTATED     8   0   0   1
  FLCN WILD-TYPE 302  11   4  24
D140V13, multiclass
    clus
vv   FLCN MUTATED FLCN WILD-TYPE
  R0            8            302
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLCN MUTATED                                  0     0
  FLCN WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLCN MUTATED                           0     8
  FLCN WILD-TYPE                        29   369
D140V14, multiclass
                                  clus
vv                                 FLCN MUTATED FLCN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V15, binary
                cls
clus               0   1
  FLCN MUTATED     0   6
  FLCN WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      0    6
  FLCN WILD-TYPE    6  343
                        clus
vv                       FLCN MUTATED FLCN WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(141) Variable = C2ORF53 MUTATION ANALYSIS
D141V1, survival
                   sevent
clus2                 0   1
  C2ORF53 MUTATED    11   1
  C2ORF53 WILD-TYPE 304 140
  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
               12               444 
  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
                1               140 
$`C2ORF53 MUTATED`
TCGA-05-4382 TCGA-05-4427 TCGA-44-7670 TCGA-50-5933 TCGA-55-6987 TCGA-55-7995 
       19.96        26.01        29.00        78.67        70.26         0.16 
TCGA-55-8207 TCGA-55-8506 TCGA-62-8399 TCGA-64-5779 TCGA-95-7039 TCGA-MN-A4N4 
        2.17         0.36        88.64        28.41         1.12        38.63 

$`C2ORF53 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
        0.53         6.48        17.65         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 
       23.64        15.65        17.98         1.08         1.51        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        6.12        23.61         1.08        19.00        17.29         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
             0.16              0.00 
  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
            88.64            223.96 
  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
           27.210            17.835 
[1] "0.2 - 88.6 (27.2)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "5.9"
D141V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C2ORF53 MUTATED         0        3        2         1         3          3
  C2ORF53 WILD-TYPE       4      120      131        45        64         67
                   vv
clus                STAGE IIIB STAGE IV
  C2ORF53 MUTATED            1        0
  C2ORF53 WILD-TYPE         10       25
D141V3, multiclass
            clus
vv           C2ORF53 MUTATED C2ORF53 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 3               120
  STAGE IB                 2               131
  STAGE IIA                1                45
  STAGE IIB                3                64
  STAGE IIIA               3                67
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF53 MUTATED     4   5   3   1
  C2ORF53 WILD-TYPE 151 256  40  17
D141V4, multiclass
    clus
vv   C2ORF53 MUTATED C2ORF53 WILD-TYPE
  T1               4               151
  T2               5               256
  T3               3                40
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  C2ORF53 MUTATED     7   2     4
  C2ORF53 WILD-TYPE 300  87    68
D141V5, multiclass
       clus
vv      C2ORF53 MUTATED C2ORF53 WILD-TYPE
  N0                  7               300
  N1                  2                87
  N2+N3               4                68
[1] 3 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
  C2ORF53 MUTATED    10   0
  C2ORF53 WILD-TYPE 317  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF53 MUTATED     10    0
  C2ORF53 WILD-TYPE  317   23
   clus
vv  C2ORF53 MUTATED C2ORF53 WILD-TYPE
  0              10               317
  1               0                23
[1] 2 2
[1] FALSE
D141V7, binary
                   cls
clus                  0   1
  C2ORF53 MUTATED     6   7
  C2ORF53 WILD-TYPE 253 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF53 MUTATED      6    7
  C2ORF53 WILD-TYPE  253  214
        clus
vv       C2ORF53 MUTATED C2ORF53 WILD-TYPE
  FEMALE               6               253
  MALE                 7               214
[1] 2 2
[1] FALSE
D141V8, continuous
[1] "Remove cluster labels:" "C2ORF53 MUTATED"       
clus
  C2ORF53 MUTATED C2ORF53 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8402        TCGA-62-A46O 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N5 
"C2ORF53 WILD-TYPE" "C2ORF53 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  C2ORF53 MUTATED                            2
  C2ORF53 WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  C2ORF53 MUTATED                                   3
  C2ORF53 WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C2ORF53 MUTATED                                                    6
  C2ORF53 WILD-TYPE                                                288
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C2ORF53 MUTATED                                            0
  C2ORF53 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C2ORF53 MUTATED                                               0
  C2ORF53 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  C2ORF53 MUTATED                                0
  C2ORF53 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  C2ORF53 MUTATED                                    0
  C2ORF53 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C2ORF53 MUTATED                              0                             2
  C2ORF53 WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C2ORF53 MUTATED                                               0
  C2ORF53 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  C2ORF53 MUTATED                              0
  C2ORF53 WILD-TYPE                            9
D141V9, multiclass
                                                    clus
vv                                                   C2ORF53 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   C2ORF53 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V10, binary
                   cls
clus                  0   1
  C2ORF53 MUTATED     2  11
  C2ORF53 WILD-TYPE  18 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF53 MUTATED      2   11
  C2ORF53 WILD-TYPE   18  449
     clus
vv    C2ORF53 MUTATED C2ORF53 WILD-TYPE
  NO                2                18
  YES              11               449
[1] 2 2
[1] FALSE
D141V11, continuous
D141V12, continuous
                   vv
clus                 R0  R1  R2  RX
  C2ORF53 MUTATED     8   0   1   0
  C2ORF53 WILD-TYPE 302  11   3  25
D141V13, multiclass
    clus
vv   C2ORF53 MUTATED C2ORF53 WILD-TYPE
  R0               8               302
  R1               0                11
  R2               1                 3
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C2ORF53 MUTATED                                  0     0
  C2ORF53 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C2ORF53 MUTATED                           0    10
  C2ORF53 WILD-TYPE                        29   367
D141V14, multiclass
                                  clus
vv                                 C2ORF53 MUTATED C2ORF53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                         10               367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V15, binary
                   cls
clus                  0   1
  C2ORF53 MUTATED     1   9
  C2ORF53 WILD-TYPE   5 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF53 MUTATED      1    9
  C2ORF53 WILD-TYPE    5  340
                        clus
vv                       C2ORF53 MUTATED C2ORF53 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               9               340
[1] 2 2
[1] FALSE

Clustering(142) Variable = C1ORF177 MUTATION ANALYSIS
D142V1, survival
                    sevent
clus2                  0   1
  C1ORF177 MUTATED     5   2
  C1ORF177 WILD-TYPE 310 139
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                 7                449 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                 2                139 
$`C1ORF177 MUTATED`
TCGA-05-4397 TCGA-44-6778 TCGA-55-8507 TCGA-55-8511 TCGA-86-7711 TCGA-95-7947 
       24.03        61.28         0.26         0.30        34.39        15.68 
TCGA-NJ-A4YF 
       71.05 

$`C1ORF177 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.36         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        19.13        73.91        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
              0.26               0.00 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
             71.05             223.96 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
             24.03              17.98 
[1] "0.3 - 71.0 (24.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D142V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C1ORF177 MUTATED         0        4        1         1         1          1
  C1ORF177 WILD-TYPE       4      119      132        45        66         69
                    vv
clus                 STAGE IIIB STAGE IV
  C1ORF177 MUTATED            0        1
  C1ORF177 WILD-TYPE         11       24
D142V3, multiclass
            clus
vv           C1ORF177 MUTATED C1ORF177 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  4                119
  STAGE IB                  1                132
  STAGE IIA                 1                 45
  STAGE IIB                 1                 66
  STAGE IIIA                1                 69
  STAGE IIIB                0                 11
  STAGE IV                  1                 24
[1] 8 2
[1] TRUE
[1] "dimension of 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     4   5   0   0
  C1ORF177 WILD-TYPE 151 256  43  18
D142V4, multiclass
    clus
vv   C1ORF177 MUTATED C1ORF177 WILD-TYPE
  T1                4                151
  T2                5                256
  T3                0                 43
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  C1ORF177 MUTATED     5   2     2
  C1ORF177 WILD-TYPE 302  87    70
D142V5, multiclass
       clus
vv      C1ORF177 MUTATED C1ORF177 WILD-TYPE
  N0                   5                302
  N1                   2                 87
  N2+N3                2                 70
[1] 3 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
  C1ORF177 MUTATED     5   1
  C1ORF177 WILD-TYPE 322  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      5    1
  C1ORF177 WILD-TYPE  322   22
   clus
vv  C1ORF177 MUTATED C1ORF177 WILD-TYPE
  0                5                322
  1                1                 22
[1] 2 2
[1] FALSE
D142V7, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED     3   6
  C1ORF177 WILD-TYPE 256 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      3    6
  C1ORF177 WILD-TYPE  256  215
        clus
vv       C1ORF177 MUTATED C1ORF177 WILD-TYPE
  FEMALE                3                256
  MALE                  6                215
[1] 2 2
[1] FALSE
D142V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  C1ORF177 MUTATED                            0
  C1ORF177 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  C1ORF177 MUTATED                                   3
  C1ORF177 WILD-TYPE                                99
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C1ORF177 MUTATED                                                    6
  C1ORF177 WILD-TYPE                                                288
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C1ORF177 MUTATED                                            0
  C1ORF177 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C1ORF177 MUTATED                                               0
  C1ORF177 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  C1ORF177 MUTATED                                0
  C1ORF177 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  C1ORF177 MUTATED                                    0
  C1ORF177 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C1ORF177 MUTATED                              0                             0
  C1ORF177 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C1ORF177 MUTATED                                               0
  C1ORF177 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  C1ORF177 MUTATED                              0
  C1ORF177 WILD-TYPE                            9
D142V9, multiclass
                                                    clus
vv                                                   C1ORF177 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   C1ORF177 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V10, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED     0   9
  C1ORF177 WILD-TYPE  20 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      0    9
  C1ORF177 WILD-TYPE   20  451
     clus
vv    C1ORF177 MUTATED C1ORF177 WILD-TYPE
  NO                 0                 20
  YES                9                451
[1] 2 2
[1] FALSE
D142V11, continuous
D142V12, continuous
                    vv
clus                  R0  R1  R2  RX
  C1ORF177 MUTATED     6   0   0   1
  C1ORF177 WILD-TYPE 304  11   4  24
D142V13, multiclass
    clus
vv   C1ORF177 MUTATED C1ORF177 WILD-TYPE
  R0                6                304
  R1                0                 11
  R2                0                  4
  RX                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF177 MUTATED                                  0     0
  C1ORF177 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF177 MUTATED                           2     4
  C1ORF177 WILD-TYPE                        27   373
D142V14, multiclass
                                  clus
vv                                 C1ORF177 MUTATED C1ORF177 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       2                 27
  WHITE                                           4                373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V15, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED     1   4
  C1ORF177 WILD-TYPE   5 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      1    4
  C1ORF177 WILD-TYPE    5  345
                        clus
vv                       C1ORF177 MUTATED C1ORF177 WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO                4                345
[1] 2 2
[1] FALSE

Clustering(143) Variable = STK19 MUTATION ANALYSIS
D143V1, survival
                 sevent
clus2               0   1
  STK19 MUTATED     3   2
  STK19 WILD-TYPE 312 139
  STK19 MUTATED STK19 WILD-TYPE 
              5             451 
  STK19 MUTATED STK19 WILD-TYPE 
              2             139 
$`STK19 MUTATED`
TCGA-55-8506 TCGA-62-A46Y TCGA-69-7979 TCGA-86-8671 TCGA-MP-A4TF 
        0.36        13.61         2.93        27.58        11.05 

$`STK19 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        67.96        72.30        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 
       21.47        14.60         1.15        13.91        30.84         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  STK19 MUTATED STK19 WILD-TYPE 
           0.36            0.00 
  STK19 MUTATED STK19 WILD-TYPE 
          27.58          223.96 
  STK19 MUTATED STK19 WILD-TYPE 
          11.05           18.12 
[1] "0.4 - 27.6 (11.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "3.3"
D143V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STK19 MUTATED         0        0        1         1         2          1
  STK19 WILD-TYPE       4      123      132        45        65         69
                 vv
clus              STAGE IIIB STAGE IV
  STK19 MUTATED            0        0
  STK19 WILD-TYPE         11       25
D143V3, multiclass
            clus
vv           STK19 MUTATED STK19 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               1             132
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK19 MUTATED     0   4   1   0
  STK19 WILD-TYPE 155 257  42  18
D143V4, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  T1             0             155
  T2             4             257
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  STK19 MUTATED     3   1     1
  STK19 WILD-TYPE 304  88    71
D143V5, multiclass
       clus
vv      STK19 MUTATED STK19 WILD-TYPE
  N0                3             304
  N1                1              88
  N2+N3             1              71
[1] 3 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
  STK19 MUTATED     3   0
  STK19 WILD-TYPE 324  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      3    0
  STK19 WILD-TYPE  324   23
   clus
vv  STK19 MUTATED STK19 WILD-TYPE
  0             3             324
  1             0              23
[1] 2 2
[1] FALSE
D143V7, binary
                 cls
clus                0   1
  STK19 MUTATED     5   0
  STK19 WILD-TYPE 254 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      5    0
  STK19 WILD-TYPE  254  221
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             5             254
  MALE               0             221
[1] 2 2
[1] FALSE
D143V8, continuous
[1] "Remove cluster labels:" "STK19 MUTATED"         
clus
  STK19 MUTATED STK19 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A470      TCGA-62-A471 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-A4JF 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STK19 MUTATED                            1                                 1
  STK19 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STK19 MUTATED                                                    2
  STK19 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STK19 MUTATED                                            0
  STK19 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STK19 MUTATED                                               0
  STK19 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STK19 MUTATED                                0
  STK19 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STK19 MUTATED                                    0
  STK19 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STK19 MUTATED                              0                             1
  STK19 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STK19 MUTATED                                               0
  STK19 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STK19 MUTATED                              0
  STK19 WILD-TYPE                            9
D143V9, multiclass
                                                    clus
vv                                                   STK19 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STK19 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V10, binary
                 cls
clus                0   1
  STK19 MUTATED     0   5
  STK19 WILD-TYPE  20 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0    5
  STK19 WILD-TYPE   20  455
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              0              20
  YES             5             455
[1] 2 2
[1] FALSE
D143V11, continuous
[1] "Remove cluster labels:" "STK19 MUTATED"         
clus
  STK19 MUTATED STK19 WILD-TYPE 
              2             331 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4396 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4397      TCGA-05-4398      TCGA-05-4405      TCGA-05-4410 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4415      TCGA-05-4417      TCGA-05-4418      TCGA-05-4420 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4422      TCGA-05-4424      TCGA-05-4425      TCGA-05-4426 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4430      TCGA-05-4432      TCGA-05-4433 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4434      TCGA-05-5420      TCGA-05-5423      TCGA-05-5425 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-5428      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-38-4625      TCGA-38-4626      TCGA-38-4629      TCGA-38-4631 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-38-4632      TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-3396      TCGA-44-3398      TCGA-44-3918 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-4112      TCGA-44-5643      TCGA-44-5644      TCGA-44-5645 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6145      TCGA-44-6146      TCGA-44-6148 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6774      TCGA-44-6775      TCGA-44-6776      TCGA-44-6777 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6778      TCGA-44-6779      TCGA-44-7659      TCGA-44-7660 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-7661      TCGA-44-7662      TCGA-44-7667      TCGA-44-7669 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-7670      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4490      TCGA-49-4494 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4507      TCGA-49-4510 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4514      TCGA-49-6742      TCGA-49-6743      TCGA-49-6744 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-6745      TCGA-49-6761      TCGA-49-6767      TCGA-50-5051 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-5072      TCGA-50-5931      TCGA-50-5939      TCGA-50-5941 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-5942      TCGA-50-6590      TCGA-50-7109      TCGA-50-8457 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-8459      TCGA-53-7624      TCGA-53-7626      TCGA-53-7813 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-6543      TCGA-55-6971      TCGA-55-6983 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-6985      TCGA-55-7281      TCGA-55-7283      TCGA-55-7574 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7724      TCGA-55-7725      TCGA-55-7726      TCGA-55-7728 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7903      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-7994      TCGA-55-7995      TCGA-55-8089 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8203      TCGA-55-8205      TCGA-55-8208      TCGA-55-8299 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8301      TCGA-55-8302      TCGA-55-8507      TCGA-55-8511 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8514      TCGA-55-8614      TCGA-55-8615 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-A46O      TCGA-62-A46P 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A470      TCGA-62-A471 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1676      TCGA-64-1677      TCGA-64-1679 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5774      TCGA-64-5775      TCGA-64-5778      TCGA-64-5779 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5781      TCGA-64-5815      TCGA-69-7761      TCGA-69-7763 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-7764      TCGA-69-7973      TCGA-69-7974      TCGA-69-7978 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-7980      TCGA-69-8253      TCGA-69-8254      TCGA-69-8255 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4658      TCGA-73-4659      TCGA-73-4662 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4668      TCGA-73-4670      TCGA-73-4675 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-75-5122      TCGA-75-5125 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-75-5126      TCGA-75-6203      TCGA-75-6206      TCGA-75-6207 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-75-6211      TCGA-75-6214      TCGA-75-7027      TCGA-75-7031 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-80-5608      TCGA-80-5611      TCGA-83-5908      TCGA-86-6851 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7714      TCGA-86-7954 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8673      TCGA-86-8674      TCGA-91-6829 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-6830      TCGA-91-6835      TCGA-91-6836      TCGA-91-6840 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-6849      TCGA-91-7771      TCGA-91-8499      TCGA-91-A4BC 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-95-7039      TCGA-95-7043      TCGA-95-7562 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-95-7944      TCGA-95-7947      TCGA-95-7948      TCGA-95-A4VK 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-95-A4VN      TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-7552      TCGA-97-7553      TCGA-97-7554      TCGA-97-7937 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-7938      TCGA-97-7941      TCGA-97-8171      TCGA-97-8172 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-8174      TCGA-97-8176      TCGA-97-8179      TCGA-97-A4LX 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2      TCGA-97-A4M3 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-A4M5      TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-99-8028      TCGA-99-8032      TCGA-J2-8194      TCGA-J2-A4AD 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6      TCGA-L9-A443 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-L9-A444      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4T8      TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TH      TCGA-MP-A4TI 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YF      TCGA-NJ-A4YG 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ      TCGA-NJ-A55A 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
D143V12, continuous
                 vv
clus               R0  R1  R2  RX
  STK19 MUTATED     4   0   0   0
  STK19 WILD-TYPE 306  11   4  25
D143V13, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK19 MUTATED                                  0     0
  STK19 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK19 MUTATED                           0     5
  STK19 WILD-TYPE                        29   372
D143V14, multiclass
                                  clus
vv                                 STK19 MUTATED STK19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V15, binary
                 cls
clus                0   1
  STK19 MUTATED     0   5
  STK19 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0    5
  STK19 WILD-TYPE    6  344
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(144) Variable = PKD2 MUTATION ANALYSIS
D144V1, survival
                sevent
clus2              0   1
  PKD2 MUTATED    11   1
  PKD2 WILD-TYPE 304 140
  PKD2 MUTATED PKD2 WILD-TYPE 
            12            444 
  PKD2 MUTATED PKD2 WILD-TYPE 
             1            140 
$`PKD2 MUTATED`
TCGA-05-4417 TCGA-05-5428 TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 TCGA-44-8120 
       14.96        22.03        12.03        18.87        29.00         8.55 
TCGA-55-7995 TCGA-64-5778 TCGA-69-7978 TCGA-86-8073 TCGA-93-A4JN TCGA-NJ-A4YF 
        0.16        42.90         2.30        24.33        23.61        71.05 

$`PKD2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 
       16.44        14.60        19.46         7.17        36.07        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
        6.12         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  PKD2 MUTATED PKD2 WILD-TYPE 
          0.16           0.00 
  PKD2 MUTATED PKD2 WILD-TYPE 
         71.05         223.96 
  PKD2 MUTATED PKD2 WILD-TYPE 
         20.45          17.95 
[1] "0.2 - 71.0 (20.5)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "3.6"
D144V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PKD2 MUTATED         0        3        7         3         1          0
  PKD2 WILD-TYPE       4      120      126        43        66         70
                vv
clus             STAGE IIIB STAGE IV
  PKD2 MUTATED            0        1
  PKD2 WILD-TYPE         11       24
D144V3, multiclass
            clus
vv           PKD2 MUTATED PKD2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              7            126
  STAGE IIA             3             43
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PKD2 MUTATED     6   9   0   0
  PKD2 WILD-TYPE 149 252  43  18
D144V4, multiclass
    clus
vv   PKD2 MUTATED PKD2 WILD-TYPE
  T1            6            149
  T2            9            252
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  PKD2 MUTATED    10   4     0
  PKD2 WILD-TYPE 297  85    72
D144V5, multiclass
       clus
vv      PKD2 MUTATED PKD2 WILD-TYPE
  N0              10            297
  N1               4             85
  N2+N3            0             72
[1] 3 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
  PKD2 MUTATED    12   1
  PKD2 WILD-TYPE 315  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED     12    1
  PKD2 WILD-TYPE  315   22
   clus
vv  PKD2 MUTATED PKD2 WILD-TYPE
  0           12            315
  1            1             22
[1] 2 2
[1] FALSE
D144V7, binary
                cls
clus               0   1
  PKD2 MUTATED     6   9
  PKD2 WILD-TYPE 253 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      6    9
  PKD2 WILD-TYPE  253  212
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  FEMALE            6            253
  MALE              9            212
[1] 2 2
[1] FALSE
D144V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PKD2 MUTATED                            1                                 5
  PKD2 WILD-TYPE                         17                                97
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PKD2 MUTATED                                                    7
  PKD2 WILD-TYPE                                                287
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PKD2 MUTATED                                            0
  PKD2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PKD2 MUTATED                                               2
  PKD2 WILD-TYPE                                            17
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  PKD2 MUTATED                                0
  PKD2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  PKD2 MUTATED                                    0
  PKD2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PKD2 MUTATED                              0                             0
  PKD2 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PKD2 MUTATED                                               0
  PKD2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  PKD2 MUTATED                              0
  PKD2 WILD-TYPE                            9
D144V9, multiclass
                                                    clus
vv                                                   PKD2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 2
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   PKD2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V10, binary
                cls
clus               0   1
  PKD2 MUTATED     0  15
  PKD2 WILD-TYPE  20 445
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      0   15
  PKD2 WILD-TYPE   20  445
     clus
vv    PKD2 MUTATED PKD2 WILD-TYPE
  NO             0             20
  YES           15            445
[1] 2 2
[1] FALSE
D144V11, continuous
D144V12, continuous
                vv
clus              R0  R1  R2  RX
  PKD2 MUTATED     6   0   0   2
  PKD2 WILD-TYPE 304  11   4  23
D144V13, multiclass
    clus
vv   PKD2 MUTATED PKD2 WILD-TYPE
  R0            6            304
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKD2 MUTATED                                  0     0
  PKD2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PKD2 MUTATED                           3     8
  PKD2 WILD-TYPE                        26   369
D144V14, multiclass
                                  clus
vv                                 PKD2 MUTATED PKD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   3             26
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V15, binary
                cls
clus               0   1
  PKD2 MUTATED     1  10
  PKD2 WILD-TYPE   5 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      1   10
  PKD2 WILD-TYPE    5  339
                        clus
vv                       PKD2 MUTATED PKD2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(145) Variable = NOTCH4 MUTATION ANALYSIS
D145V1, survival
                  sevent
clus2                0   1
  NOTCH4 MUTATED    25  16
  NOTCH4 WILD-TYPE 290 125
  NOTCH4 MUTATED NOTCH4 WILD-TYPE 
              41              415 
  NOTCH4 MUTATED NOTCH4 WILD-TYPE 
              16              125 
$`NOTCH4 MUTATED`
TCGA-05-4250 TCGA-05-4398 TCGA-05-4420 TCGA-05-4432 TCGA-38-4625 TCGA-38-4629 
        3.98        47.05        29.98        25.02        97.74        28.41 
TCGA-38-4631 TCGA-44-2656 TCGA-44-3918 TCGA-44-7662 TCGA-44-7670 TCGA-50-5049 
       11.64        46.98        34.06         7.17        29.00        70.55 
TCGA-50-5051 TCGA-50-5941 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 
       15.72        18.64         0.53         6.48        19.82         0.16 
TCGA-55-A494 TCGA-62-8398 TCGA-64-5781 TCGA-67-6217 TCGA-73-4658 TCGA-73-4677 
       15.81        14.60        51.25        13.87        52.60         1.25 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7155 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 
       20.58        21.90        38.50       110.50         5.88        34.39 
TCGA-86-7714 TCGA-95-7039 TCGA-95-8039 TCGA-97-7554 TCGA-97-8172 TCGA-99-8025 
       20.55         1.12        27.29        25.48        17.92        34.85 
TCGA-L9-A443 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-NJ-A55R 
        3.81         2.43        10.09        11.05        19.82 

$`NOTCH4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 
        8.68       120.79        37.71        49.05        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       14.60        19.46        12.03        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       71.47        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 
        1.78         1.45        18.64        17.65         6.15        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.04         5.72         4.64         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        1.32         5.39        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        5.69        19.27        35.93        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       39.75        77.59        10.55        27.09        12.36        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       13.87        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.68        15.65         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        63.52        43.79         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 
       35.47        16.44        19.00        14.30         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-O1-A52J 
       59.11 

  NOTCH4 MUTATED NOTCH4 WILD-TYPE 
            0.16             0.00 
  NOTCH4 MUTATED NOTCH4 WILD-TYPE 
          110.50           223.96 
  NOTCH4 MUTATED NOTCH4 WILD-TYPE 
           19.82            17.72 
[1] "0.2 - 110.5 (19.8)" "0.0 - 224.0 (17.7)"
[1] "hr=" "1.1"
D145V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NOTCH4 MUTATED         0        7       12         7         6         10
  NOTCH4 WILD-TYPE       4      116      121        39        61         60
                  vv
clus               STAGE IIIB STAGE IV
  NOTCH4 MUTATED            1        0
  NOTCH4 WILD-TYPE         10       25
D145V3, multiclass
            clus
vv           NOTCH4 MUTATED NOTCH4 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                7              116
  STAGE IB               12              121
  STAGE IIA               7               39
  STAGE IIB               6               61
  STAGE IIIA             10               60
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NOTCH4 MUTATED     9  28   5   1
  NOTCH4 WILD-TYPE 146 233  38  17
D145V4, multiclass
    clus
vv   NOTCH4 MUTATED NOTCH4 WILD-TYPE
  T1              9              146
  T2             28              233
  T3              5               38
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  NOTCH4 MUTATED    24   9    10
  NOTCH4 WILD-TYPE 283  80    62
D145V5, multiclass
       clus
vv      NOTCH4 MUTATED NOTCH4 WILD-TYPE
  N0                24              283
  N1                 9               80
  N2+N3             10               62
[1] 3 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
  NOTCH4 MUTATED    35   0
  NOTCH4 WILD-TYPE 292  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH4 MUTATED     35    0
  NOTCH4 WILD-TYPE  292   23
   clus
vv  NOTCH4 MUTATED NOTCH4 WILD-TYPE
  0             35              292
  1              0               23
[1] 2 2
[1] FALSE
D145V7, binary
                  cls
clus                 0   1
  NOTCH4 MUTATED    24  19
  NOTCH4 WILD-TYPE 235 202
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH4 MUTATED     24   19
  NOTCH4 WILD-TYPE  235  202
        clus
vv       NOTCH4 MUTATED NOTCH4 WILD-TYPE
  FEMALE             24              235
  MALE               19              202
[1] 2 2
[1] FALSE
D145V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NOTCH4 MUTATED                            2                                10
  NOTCH4 WILD-TYPE                         16                                92
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NOTCH4 MUTATED                                                   30
  NOTCH4 WILD-TYPE                                                264
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NOTCH4 MUTATED                                            0
  NOTCH4 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NOTCH4 MUTATED                                               0
  NOTCH4 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  NOTCH4 MUTATED                                0
  NOTCH4 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  NOTCH4 MUTATED                                    0
  NOTCH4 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NOTCH4 MUTATED                              0                             1
  NOTCH4 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NOTCH4 MUTATED                                               0
  NOTCH4 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  NOTCH4 MUTATED                              0
  NOTCH4 WILD-TYPE                            9
D145V9, multiclass
                                                    clus
vv                                                   NOTCH4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   NOTCH4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              264
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V10, binary
                  cls
clus                 0   1
  NOTCH4 MUTATED     2  41
  NOTCH4 WILD-TYPE  18 419
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH4 MUTATED      2   41
  NOTCH4 WILD-TYPE   18  419
     clus
vv    NOTCH4 MUTATED NOTCH4 WILD-TYPE
  NO               2               18
  YES             41              419
[1] 2 2
[1] FALSE
D145V11, continuous
D145V12, continuous
                  vv
clus                R0  R1  R2  RX
  NOTCH4 MUTATED    30   0   1   3
  NOTCH4 WILD-TYPE 280  11   3  22
D145V13, multiclass
    clus
vv   NOTCH4 MUTATED NOTCH4 WILD-TYPE
  R0             30              280
  R1              0               11
  R2              1                3
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH4 MUTATED                                  0     0
  NOTCH4 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NOTCH4 MUTATED                           3    33
  NOTCH4 WILD-TYPE                        26   344
D145V14, multiclass
                                  clus
vv                                 NOTCH4 MUTATED NOTCH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                        33              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V15, binary
                  cls
clus                 0   1
  NOTCH4 MUTATED     2  29
  NOTCH4 WILD-TYPE   4 320
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH4 MUTATED      2   29
  NOTCH4 WILD-TYPE    4  320
                        clus
vv                       NOTCH4 MUTATED NOTCH4 WILD-TYPE
  HISPANIC OR LATINO                  2                4
  NOT HISPANIC OR LATINO             29              320
[1] 2 2
[1] FALSE

Clustering(146) Variable = COL15A1 MUTATION ANALYSIS
D146V1, survival
                   sevent
clus2                 0   1
  COL15A1 MUTATED    25   5
  COL15A1 WILD-TYPE 290 136
  COL15A1 MUTATED COL15A1 WILD-TYPE 
               30               426 
  COL15A1 MUTATED COL15A1 WILD-TYPE 
                5               136 
$`COL15A1 MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4405 TCGA-05-4424 TCGA-05-5423 TCGA-35-4123 
       19.96        37.02        20.05        30.02         4.96         5.98 
TCGA-38-4626 TCGA-38-4631 TCGA-44-2656 TCGA-44-3918 TCGA-49-6761 TCGA-50-6592 
      120.79        11.64        46.98        34.06        11.64        25.55 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6971 TCGA-55-7907 TCGA-55-7994 TCGA-55-8616 
       23.05        48.62         0.82         0.53        19.82         1.58 
TCGA-55-8620 TCGA-64-5775 TCGA-64-5781 TCGA-78-7158 TCGA-86-8073 TCGA-86-8673 
        2.17         2.04        51.25         5.88        24.33        14.96 
TCGA-91-A4BC TCGA-93-A4JP TCGA-97-7554 TCGA-99-7458 TCGA-L9-A444 TCGA-MN-A4N4 
        1.45        19.00        25.48        24.56         0.20        38.63 

$`COL15A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
       24.03        47.05         8.02        19.00         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        9.01        29.98        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 
       25.02        25.02        24.00        15.02        15.02        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
       22.03         9.04         2.04         7.40         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 
       14.63        12.13        29.26        17.16        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
       42.35         3.91        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94         9.21         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 
        0.79        42.51        40.73        15.25        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
        1.45        18.64         6.48        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 
        4.80         6.64        17.62         0.49         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       87.98        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       32.09        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       16.70        24.49         4.08         4.57         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
        1.15        13.91        30.84        27.58         0.62        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       19.89        31.69        64.60        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        3.81        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  COL15A1 MUTATED COL15A1 WILD-TYPE 
              0.2               0.0 
  COL15A1 MUTATED COL15A1 WILD-TYPE 
           120.79            223.96 
  COL15A1 MUTATED COL15A1 WILD-TYPE 
           19.890            17.835 
[1] "0.2 - 120.8 (19.9)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.9"
D146V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL15A1 MUTATED         0        6       12         3         3          4
  COL15A1 WILD-TYPE       4      117      121        43        64         66
                   vv
clus                STAGE IIIB STAGE IV
  COL15A1 MUTATED            1        2
  COL15A1 WILD-TYPE         10       23
D146V3, multiclass
            clus
vv           COL15A1 MUTATED COL15A1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 6               117
  STAGE IB                12               121
  STAGE IIA                3                43
  STAGE IIB                3                64
  STAGE IIIA               4                66
  STAGE IIIB               1                10
  STAGE IV                 2                23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL15A1 MUTATED     7  18   2   3
  COL15A1 WILD-TYPE 148 243  41  15
D146V4, multiclass
    clus
vv   COL15A1 MUTATED COL15A1 WILD-TYPE
  T1               7               148
  T2              18               243
  T3               2                41
  T4               3                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"
                   vv
clus                 N0  N1 N2+N3
  COL15A1 MUTATED    24   3     3
  COL15A1 WILD-TYPE 283  86    69
D146V5, multiclass
       clus
vv      COL15A1 MUTATED COL15A1 WILD-TYPE
  N0                 24               283
  N1                  3                86
  N2+N3               3                69
[1] 3 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
  COL15A1 MUTATED    23   2
  COL15A1 WILD-TYPE 304  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL15A1 MUTATED     23    2
  COL15A1 WILD-TYPE  304   21
   clus
vv  COL15A1 MUTATED COL15A1 WILD-TYPE
  0              23               304
  1               2                21
[1] 2 2
[1] FALSE
D146V7, binary
                   cls
clus                  0   1
  COL15A1 MUTATED    15  16
  COL15A1 WILD-TYPE 244 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL15A1 MUTATED     15   16
  COL15A1 WILD-TYPE  244  205
        clus
vv       COL15A1 MUTATED COL15A1 WILD-TYPE
  FEMALE              15               244
  MALE                16               205
[1] 2 2
[1] FALSE
D146V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  COL15A1 MUTATED                            0
  COL15A1 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL15A1 MUTATED                                   7
  COL15A1 WILD-TYPE                                95
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL15A1 MUTATED                                                   18
  COL15A1 WILD-TYPE                                                276
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL15A1 MUTATED                                            0
  COL15A1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL15A1 MUTATED                                               3
  COL15A1 WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  COL15A1 MUTATED                                1
  COL15A1 WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  COL15A1 MUTATED                                    0
  COL15A1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL15A1 MUTATED                              0                             2
  COL15A1 WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL15A1 MUTATED                                               0
  COL15A1 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  COL15A1 MUTATED                              0
  COL15A1 WILD-TYPE                            9
D146V9, multiclass
                                                    clus
vv                                                   COL15A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              18
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   COL15A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V10, binary
                   cls
clus                  0   1
  COL15A1 MUTATED     0  31
  COL15A1 WILD-TYPE  20 429
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL15A1 MUTATED      0   31
  COL15A1 WILD-TYPE   20  429
     clus
vv    COL15A1 MUTATED COL15A1 WILD-TYPE
  NO                0                20
  YES              31               429
[1] 2 2
[1] FALSE
D146V11, continuous
D146V12, continuous
                   vv
clus                 R0  R1  R2  RX
  COL15A1 MUTATED    24   2   0   1
  COL15A1 WILD-TYPE 286   9   4  24
D146V13, multiclass
    clus
vv   COL15A1 MUTATED COL15A1 WILD-TYPE
  R0              24               286
  R1               2                 9
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL15A1 MUTATED                                  0     2
  COL15A1 WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COL15A1 MUTATED                           0    23
  COL15A1 WILD-TYPE                        29   354
D146V14, multiclass
                                  clus
vv                                 COL15A1 MUTATED COL15A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                         23               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V15, binary
                   cls
clus                  0   1
  COL15A1 MUTATED     0  23
  COL15A1 WILD-TYPE   6 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL15A1 MUTATED      0   23
  COL15A1 WILD-TYPE    6  326
                        clus
vv                       COL15A1 MUTATED COL15A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              23               326
[1] 2 2
[1] FALSE

Clustering(147) Variable = SOS2 MUTATION ANALYSIS
D147V1, survival
                sevent
clus2              0   1
  SOS2 MUTATED     9   4
  SOS2 WILD-TYPE 306 137
  SOS2 MUTATED SOS2 WILD-TYPE 
            13            443 
  SOS2 MUTATED SOS2 WILD-TYPE 
             4            137 
$`SOS2 MUTATED`
TCGA-05-4418 TCGA-05-5423 TCGA-38-4631 TCGA-49-4506 TCGA-49-6743 TCGA-62-8399 
        9.01         4.96        11.64        32.84        12.13        88.64 
TCGA-69-7978 TCGA-86-8278 TCGA-91-6835 TCGA-95-7567 TCGA-95-A4VN TCGA-L9-A444 
        2.30        15.65         2.60        18.67        18.18         0.20 
TCGA-MP-A4SV 
       86.14 

$`SOS2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        14.07         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       14.63        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        4.57        24.33         0.79        15.75        16.08        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         1.22         2.86        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       27.29         2.76        21.40        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19        38.63         2.76        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  SOS2 MUTATED SOS2 WILD-TYPE 
           0.2            0.0 
  SOS2 MUTATED SOS2 WILD-TYPE 
         88.64         223.96 
  SOS2 MUTATED SOS2 WILD-TYPE 
         12.13          18.12 
[1] "0.2 - 88.6 (12.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D147V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SOS2 MUTATED         0        2        2         1         5          3
  SOS2 WILD-TYPE       4      121      131        45        62         67
                vv
clus             STAGE IIIB STAGE IV
  SOS2 MUTATED            0        0
  SOS2 WILD-TYPE         11       25
D147V3, multiclass
            clus
vv           SOS2 MUTATED SOS2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              2            131
  STAGE IIA             1             45
  STAGE IIB             5             62
  STAGE IIIA            3             67
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of 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     3   9   1   0
  SOS2 WILD-TYPE 152 252  42  18
D147V4, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  T1            3            152
  T2            9            252
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  SOS2 MUTATED     4   6     3
  SOS2 WILD-TYPE 303  83    69
D147V5, multiclass
       clus
vv      SOS2 MUTATED SOS2 WILD-TYPE
  N0               4            303
  N1               6             83
  N2+N3            3             69
[1] 3 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
  SOS2 MUTATED    10   0
  SOS2 WILD-TYPE 317  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     10    0
  SOS2 WILD-TYPE  317   23
   clus
vv  SOS2 MUTATED SOS2 WILD-TYPE
  0           10            317
  1            0             23
[1] 2 2
[1] FALSE
D147V7, binary
                cls
clus               0   1
  SOS2 MUTATED     7   6
  SOS2 WILD-TYPE 252 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED      7    6
  SOS2 WILD-TYPE  252  215
        clus
vv       SOS2 MUTATED SOS2 WILD-TYPE
  FEMALE            7            252
  MALE              6            215
[1] 2 2
[1] FALSE
D147V8, continuous
[1] "Remove cluster labels:" "SOS2 MUTATED"          
clus
  SOS2 MUTATED SOS2 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8402     TCGA-62-A46O 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"SOS2 WILD-TYPE" "SOS2 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SOS2 MUTATED                            0                                 4
  SOS2 WILD-TYPE                         18                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SOS2 MUTATED                                                    6
  SOS2 WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SOS2 MUTATED                                            0
  SOS2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SOS2 MUTATED                                               0
  SOS2 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SOS2 MUTATED                                1
  SOS2 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SOS2 MUTATED                                    0
  SOS2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SOS2 MUTATED                              0                             1
  SOS2 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SOS2 MUTATED                                               1
  SOS2 WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SOS2 MUTATED                              0
  SOS2 WILD-TYPE                            9
D147V9, multiclass
                                                    clus
vv                                                   SOS2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SOS2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V10, binary
                cls
clus               0   1
  SOS2 MUTATED     0  13
  SOS2 WILD-TYPE  20 447
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED      0   13
  SOS2 WILD-TYPE   20  447
     clus
vv    SOS2 MUTATED SOS2 WILD-TYPE
  NO             0             20
  YES           13            447
[1] 2 2
[1] FALSE
D147V11, continuous
D147V12, continuous
                vv
clus              R0  R1  R2  RX
  SOS2 MUTATED     9   1   0   0
  SOS2 WILD-TYPE 301  10   4  25
D147V13, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  R0            9            301
  R1            1             10
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOS2 MUTATED                                  0     0
  SOS2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SOS2 MUTATED                           0    10
  SOS2 WILD-TYPE                        29   367
D147V14, multiclass
                                  clus
vv                                 SOS2 MUTATED SOS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                      10            367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V15, binary
                cls
clus               0   1
  SOS2 MUTATED     0   9
  SOS2 WILD-TYPE   6 340
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED      0    9
  SOS2 WILD-TYPE    6  340
                        clus
vv                       SOS2 MUTATED SOS2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            9            340
[1] 2 2
[1] FALSE

Clustering(148) Variable = SETDB1 MUTATION ANALYSIS
D148V1, survival
                  sevent
clus2                0   1
  SETDB1 MUTATED     7   3
  SETDB1 WILD-TYPE 308 138
  SETDB1 MUTATED SETDB1 WILD-TYPE 
              10              446 
  SETDB1 MUTATED SETDB1 WILD-TYPE 
               3              138 
$`SETDB1 MUTATED`
TCGA-50-8457 TCGA-55-8205 TCGA-55-A493 TCGA-62-A46V TCGA-67-3771 TCGA-73-4666 
       25.61         1.08         0.92        72.30        20.05        26.30 
TCGA-86-6562 TCGA-MN-A4N4 TCGA-MP-A4T2 TCGA-MP-A4TF 
       12.36        38.63        37.35        11.05 

$`SETDB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        0.72        10.13         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
       20.71        21.40         1.58        20.58        19.59        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       67.96        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        58.45        49.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SETDB1 MUTATED SETDB1 WILD-TYPE 
            0.92             0.00 
  SETDB1 MUTATED SETDB1 WILD-TYPE 
           72.30           223.96 
  SETDB1 MUTATED SETDB1 WILD-TYPE 
           22.83            17.95 
[1] "0.9 - 72.3 (22.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D148V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SETDB1 MUTATED         0        4        2         2         1          0
  SETDB1 WILD-TYPE       4      119      131        44        66         70
                  vv
clus               STAGE IIIB STAGE IV
  SETDB1 MUTATED            0        1
  SETDB1 WILD-TYPE         11       24
D148V3, multiclass
            clus
vv           SETDB1 MUTATED SETDB1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                2              131
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SETDB1 MUTATED     5   5   0   0
  SETDB1 WILD-TYPE 150 256  43  18
D148V4, multiclass
    clus
vv   SETDB1 MUTATED SETDB1 WILD-TYPE
  T1              5              150
  T2              5              256
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  SETDB1 MUTATED     9   1     0
  SETDB1 WILD-TYPE 298  88    72
D148V5, multiclass
       clus
vv      SETDB1 MUTATED SETDB1 WILD-TYPE
  N0                 9              298
  N1                 1               88
  N2+N3              0               72
[1] 3 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
  SETDB1 MUTATED     9   1
  SETDB1 WILD-TYPE 318  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB1 MUTATED      9    1
  SETDB1 WILD-TYPE  318   22
   clus
vv  SETDB1 MUTATED SETDB1 WILD-TYPE
  0              9              318
  1              1               22
[1] 2 2
[1] FALSE
D148V7, binary
                  cls
clus                 0   1
  SETDB1 MUTATED     7   3
  SETDB1 WILD-TYPE 252 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB1 MUTATED      7    3
  SETDB1 WILD-TYPE  252  218
        clus
vv       SETDB1 MUTATED SETDB1 WILD-TYPE
  FEMALE              7              252
  MALE                3              218
[1] 2 2
[1] FALSE
D148V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SETDB1 MUTATED                            0                                 2
  SETDB1 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SETDB1 MUTATED                                                    8
  SETDB1 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SETDB1 MUTATED                                            0
  SETDB1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SETDB1 MUTATED                                               0
  SETDB1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SETDB1 MUTATED                                0
  SETDB1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SETDB1 MUTATED                                    0
  SETDB1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SETDB1 MUTATED                              0                             0
  SETDB1 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SETDB1 MUTATED                                               0
  SETDB1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SETDB1 MUTATED                              0
  SETDB1 WILD-TYPE                            9
D148V9, multiclass
                                                    clus
vv                                                   SETDB1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SETDB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V10, binary
                  cls
clus                 0   1
  SETDB1 MUTATED     1   9
  SETDB1 WILD-TYPE  19 451
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB1 MUTATED      1    9
  SETDB1 WILD-TYPE   19  451
     clus
vv    SETDB1 MUTATED SETDB1 WILD-TYPE
  NO               1               19
  YES              9              451
[1] 2 2
[1] FALSE
D148V11, continuous
D148V12, continuous
                  vv
clus                R0  R1  R2  RX
  SETDB1 MUTATED     9   0   0   0
  SETDB1 WILD-TYPE 301  11   4  25
D148V13, multiclass
    clus
vv   SETDB1 MUTATED SETDB1 WILD-TYPE
  R0              9              301
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETDB1 MUTATED                                  0     0
  SETDB1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SETDB1 MUTATED                           2     8
  SETDB1 WILD-TYPE                        27   369
D148V14, multiclass
                                  clus
vv                                 SETDB1 MUTATED SETDB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                         8              369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V15, binary
                  cls
clus                 0   1
  SETDB1 MUTATED     0  10
  SETDB1 WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB1 MUTATED      0   10
  SETDB1 WILD-TYPE    6  339
                        clus
vv                       SETDB1 MUTATED SETDB1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(149) Variable = ANTXR1 MUTATION ANALYSIS
D149V1, survival
                  sevent
clus2                0   1
  ANTXR1 MUTATED    14   4
  ANTXR1 WILD-TYPE 301 137
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              18              438 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
               4              137 
$`ANTXR1 MUTATED`
TCGA-38-4626 TCGA-49-4487 TCGA-55-7574 TCGA-55-7903 TCGA-55-7907 TCGA-55-8092 
      120.79        28.11         3.12        18.64         0.53         5.06 
TCGA-55-A491 TCGA-62-A472 TCGA-64-5779 TCGA-67-6215 TCGA-73-4668 TCGA-78-8662 
       20.58        29.92        28.41         5.72        15.35       110.50 
TCGA-97-7941 TCGA-97-8174 TCGA-99-8028 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 
        0.72         5.39        36.76        19.00         3.81         0.20 

$`ANTXR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
        0.59         1.15         7.99         0.20         0.13         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        1.45         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
       16.93        22.65        20.71        21.40         1.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.04         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        0.10        52.60        23.38        29.98        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 
       43.79        25.48         5.95         0.59        18.67        17.92 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 
       18.67        20.68        24.56        34.85         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       24.30        23.80        18.08        35.47        16.44        14.30 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
             0.2              0.0 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
          120.79           223.96 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
          16.995           18.030 
[1] "0.2 - 120.8 (17.0)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D149V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ANTXR1 MUTATED         1        7        4         3         3          1
  ANTXR1 WILD-TYPE       3      116      129        43        64         69
                  vv
clus               STAGE IIIB STAGE IV
  ANTXR1 MUTATED            0        0
  ANTXR1 WILD-TYPE         11       25
D149V3, multiclass
            clus
vv           ANTXR1 MUTATED ANTXR1 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                7              116
  STAGE IB                4              129
  STAGE IIA               3               43
  STAGE IIB               3               64
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     8   8   3   0
  ANTXR1 WILD-TYPE 147 253  40  18
D149V4, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  T1              8              147
  T2              8              253
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ANTXR1 MUTATED    16   2     1
  ANTXR1 WILD-TYPE 291  87    71
D149V5, multiclass
       clus
vv      ANTXR1 MUTATED ANTXR1 WILD-TYPE
  N0                16              291
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  ANTXR1 MUTATED    12   0
  ANTXR1 WILD-TYPE 315  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED     12    0
  ANTXR1 WILD-TYPE  315   23
   clus
vv  ANTXR1 MUTATED ANTXR1 WILD-TYPE
  0             12              315
  1              0               23
[1] 2 2
[1] FALSE
D149V7, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED    12   7
  ANTXR1 WILD-TYPE 247 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED     12    7
  ANTXR1 WILD-TYPE  247  214
        clus
vv       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  FEMALE             12              247
  MALE                7              214
[1] 2 2
[1] FALSE
D149V8, continuous
[1] "Remove cluster labels:" "ANTXR1 MUTATED"        
clus
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-62-A471       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4676 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ANTXR1 MUTATED                            2                                 0
  ANTXR1 WILD-TYPE                         16                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ANTXR1 MUTATED                                                   15
  ANTXR1 WILD-TYPE                                                279
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ANTXR1 MUTATED                                            0
  ANTXR1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ANTXR1 MUTATED                                               0
  ANTXR1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ANTXR1 MUTATED                                0
  ANTXR1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ANTXR1 MUTATED                                    1
  ANTXR1 WILD-TYPE                                  2
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ANTXR1 MUTATED                              0                             1
  ANTXR1 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ANTXR1 MUTATED                                               0
  ANTXR1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ANTXR1 MUTATED                              0
  ANTXR1 WILD-TYPE                            9
D149V9, multiclass
                                                    clus
vv                                                   ANTXR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              1
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ANTXR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V10, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     2  17
  ANTXR1 WILD-TYPE  18 443
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      2   17
  ANTXR1 WILD-TYPE   18  443
     clus
vv    ANTXR1 MUTATED ANTXR1 WILD-TYPE
  NO               2               18
  YES             17              443
[1] 2 2
[1] FALSE
D149V11, continuous
D149V12, continuous
                  vv
clus                R0  R1  R2  RX
  ANTXR1 MUTATED    17   1   0   0
  ANTXR1 WILD-TYPE 293  10   4  25
D149V13, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  R0             17              293
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANTXR1 MUTATED                                  1     0
  ANTXR1 WILD-TYPE                                0     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANTXR1 MUTATED                           1    16
  ANTXR1 WILD-TYPE                        28   361
D149V14, multiclass
                                  clus
vv                                 ANTXR1 MUTATED ANTXR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        16              361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V15, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     0  18
  ANTXR1 WILD-TYPE   6 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      0   18
  ANTXR1 WILD-TYPE    6  331
                        clus
vv                       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             18              331
[1] 2 2
[1] FALSE

Clustering(150) Variable = SLC38A8 MUTATION ANALYSIS
D150V1, survival
                   sevent
clus2                 0   1
  SLC38A8 MUTATED     5   2
  SLC38A8 WILD-TYPE 310 139
  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
                7               449 
  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
                2               139 
$`SLC38A8 MUTATED`
TCGA-44-7670 TCGA-55-7910 TCGA-64-5775 TCGA-67-3771 TCGA-78-7166 TCGA-86-8674 
       29.00         6.48         2.04        20.05         8.48        13.32 
TCGA-95-7043 
        1.22 

$`SLC38A8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
        0.79         1.78         1.45        18.64         0.53        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.12         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
             1.22              0.00 
  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
            29.00            223.96 
  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
             8.48             18.12 
[1] "1.2 - 29.0 (8.5)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "2.3"
D150V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC38A8 MUTATED         0        2        2         3         1          1
  SLC38A8 WILD-TYPE       4      121      131        43        66         69
                   vv
clus                STAGE IIIB STAGE IV
  SLC38A8 MUTATED            0        0
  SLC38A8 WILD-TYPE         11       25
D150V3, multiclass
            clus
vv           SLC38A8 MUTATED SLC38A8 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 2               131
  STAGE IIA                3                43
  STAGE IIB                1                66
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC38A8 MUTATED     3   5   0   1
  SLC38A8 WILD-TYPE 152 256  43  17
D150V4, multiclass
    clus
vv   SLC38A8 MUTATED SLC38A8 WILD-TYPE
  T1               3               152
  T2               5               256
  T3               0                43
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  SLC38A8 MUTATED     6   3     0
  SLC38A8 WILD-TYPE 301  86    72
D150V5, multiclass
       clus
vv      SLC38A8 MUTATED SLC38A8 WILD-TYPE
  N0                  6               301
  N1                  3                86
  N2+N3               0                72
[1] 3 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
  SLC38A8 MUTATED     8   0
  SLC38A8 WILD-TYPE 319  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A8 MUTATED      8    0
  SLC38A8 WILD-TYPE  319   23
   clus
vv  SLC38A8 MUTATED SLC38A8 WILD-TYPE
  0               8               319
  1               0                23
[1] 2 2
[1] FALSE
D150V7, binary
                   cls
clus                  0   1
  SLC38A8 MUTATED     5   4
  SLC38A8 WILD-TYPE 254 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A8 MUTATED      5    4
  SLC38A8 WILD-TYPE  254  217
        clus
vv       SLC38A8 MUTATED SLC38A8 WILD-TYPE
  FEMALE               5               254
  MALE                 4               217
[1] 2 2
[1] FALSE
D150V8, continuous
[1] "Remove cluster labels:" "SLC38A8 MUTATED"       
clus
  SLC38A8 MUTATED SLC38A8 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7914 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-55-8089        TCGA-55-8096        TCGA-55-8205        TCGA-55-8208 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8511        TCGA-55-8512 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" "SLC38A8 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC38A8 MUTATED                            0
  SLC38A8 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC38A8 MUTATED                                   2
  SLC38A8 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC38A8 MUTATED                                                    6
  SLC38A8 WILD-TYPE                                                288
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC38A8 MUTATED                                            0
  SLC38A8 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC38A8 MUTATED                                               0
  SLC38A8 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC38A8 MUTATED                                0
  SLC38A8 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC38A8 MUTATED                                    0
  SLC38A8 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC38A8 MUTATED                              0                             1
  SLC38A8 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC38A8 MUTATED                                               0
  SLC38A8 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC38A8 MUTATED                              0
  SLC38A8 WILD-TYPE                            9
D150V9, multiclass
                                                    clus
vv                                                   SLC38A8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SLC38A8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V10, binary
                   cls
clus                  0   1
  SLC38A8 MUTATED     1   8
  SLC38A8 WILD-TYPE  19 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A8 MUTATED      1    8
  SLC38A8 WILD-TYPE   19  452
     clus
vv    SLC38A8 MUTATED SLC38A8 WILD-TYPE
  NO                1                19
  YES               8               452
[1] 2 2
[1] FALSE
D150V11, continuous
D150V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC38A8 MUTATED     6   0   0   1
  SLC38A8 WILD-TYPE 304  11   4  24
D150V13, multiclass
    clus
vv   SLC38A8 MUTATED SLC38A8 WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC38A8 MUTATED                                  0     0
  SLC38A8 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC38A8 MUTATED                           2     5
  SLC38A8 WILD-TYPE                        27   372
D150V14, multiclass
                                  clus
vv                                 SLC38A8 MUTATED SLC38A8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                          5               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V15, binary
                   cls
clus                  0   1
  SLC38A8 MUTATED     1   5
  SLC38A8 WILD-TYPE   5 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A8 MUTATED      1    5
  SLC38A8 WILD-TYPE    5  344
                        clus
vv                       SLC38A8 MUTATED SLC38A8 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(151) Variable = COL3A1 MUTATION ANALYSIS
D151V1, survival
                  sevent
clus2                0   1
  COL3A1 MUTATED    39  13
  COL3A1 WILD-TYPE 276 128
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              52              404 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              13              128 
$`COL3A1 MUTATED`
TCGA-05-4397 TCGA-05-4398 TCGA-05-4427 TCGA-38-4631 TCGA-44-2656 TCGA-44-4112 
       24.03        47.05        26.01        11.64        46.98        26.56 
TCGA-44-5644 TCGA-44-6774 TCGA-44-7670 TCGA-44-A479 TCGA-49-4506 TCGA-49-4514 
       28.37        21.63        29.00        15.98        32.84        55.89 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5049 TCGA-50-5930 TCGA-50-5941 TCGA-50-5946 
       29.26        22.26        70.55         9.27        18.64        22.55 
TCGA-50-6593 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-6968 TCGA-55-6972 TCGA-55-6985 
       11.05        34.29         9.21        42.51        48.49        40.54 
TCGA-55-6987 TCGA-55-7907 TCGA-55-7994 TCGA-55-8089 TCGA-55-A4DG TCGA-62-8399 
       70.26         0.53        19.82         3.29        19.99        88.64 
TCGA-64-1676 TCGA-64-5781 TCGA-67-3771 TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K 
       56.81        51.25        20.05         2.93        12.56         7.04 
TCGA-73-4662 TCGA-78-7161 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8585 
       29.98         7.07        24.49         4.08        24.33         1.15 
TCGA-86-A4JF TCGA-91-6848 TCGA-97-8176 TCGA-97-A4M5 TCGA-MN-A4N4 TCGA-MP-A4T4 
       17.62         7.36        15.39        20.84        38.63        86.04 
TCGA-MP-A4TA TCGA-MP-A4TI TCGA-NJ-A4YF TCGA-NJ-A4YP 
       31.23        14.10        71.05         1.64 

$`COL3A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        0.00         9.96         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        6.25        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       14.07         8.81        29.46        29.75        14.63        12.13 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       17.16        11.64        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       21.47         8.45        15.12        29.03        25.12        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
        2.20        45.34        32.71        60.03        24.99       107.21 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        6.15         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 
       87.98         2.04        42.90        28.41        28.47        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       14.01        13.45         4.24         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       19.43        19.89        16.70         4.57         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       18.12        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        17.75        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81         0.20        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        2.43        10.09        29.46        11.05        14.66        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       73.91        62.60         0.13        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            0.53             0.00 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
           88.64           223.96 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          23.290           17.225 
[1] "0.5 - 88.6 (23.3)"  "0.0 - 224.0 (17.2)"
[1] "hr=" "1.7"
D151V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL3A1 MUTATED         1       13       13         6        10          7
  COL3A1 WILD-TYPE       3      110      120        40        57         63
                  vv
clus               STAGE IIIB STAGE IV
  COL3A1 MUTATED            1        2
  COL3A1 WILD-TYPE         10       23
D151V3, multiclass
            clus
vv           COL3A1 MUTATED COL3A1 WILD-TYPE
  STAGE I                 1                3
  STAGE IA               13              110
  STAGE IB               13              120
  STAGE IIA               6               40
  STAGE IIB              10               57
  STAGE IIIA              7               63
  STAGE IIIB              1               10
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL3A1 MUTATED    17  29   6   1
  COL3A1 WILD-TYPE 138 232  37  17
D151V4, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  T1             17              138
  T2             29              232
  T3              6               37
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  COL3A1 MUTATED    34  12     7
  COL3A1 WILD-TYPE 273  77    65
D151V5, multiclass
       clus
vv      COL3A1 MUTATED COL3A1 WILD-TYPE
  N0                34              273
  N1                12               77
  N2+N3              7               65
[1] 3 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
  COL3A1 MUTATED    39   2
  COL3A1 WILD-TYPE 288  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     39    2
  COL3A1 WILD-TYPE  288   21
   clus
vv  COL3A1 MUTATED COL3A1 WILD-TYPE
  0             39              288
  1              2               21
[1] 2 2
[1] FALSE
D151V7, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    27  26
  COL3A1 WILD-TYPE 232 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     27   26
  COL3A1 WILD-TYPE  232  195
        clus
vv       COL3A1 MUTATED COL3A1 WILD-TYPE
  FEMALE             27              232
  MALE               26              195
[1] 2 2
[1] FALSE
D151V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL3A1 MUTATED                            4                                12
  COL3A1 WILD-TYPE                         14                                90
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL3A1 MUTATED                                                   31
  COL3A1 WILD-TYPE                                                263
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL3A1 MUTATED                                            0
  COL3A1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL3A1 MUTATED                                               1
  COL3A1 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  COL3A1 MUTATED                                0
  COL3A1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  COL3A1 MUTATED                                    0
  COL3A1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL3A1 MUTATED                              0                             4
  COL3A1 WILD-TYPE                            2                            18
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL3A1 MUTATED                                               1
  COL3A1 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  COL3A1 MUTATED                              0
  COL3A1 WILD-TYPE                            9
D151V9, multiclass
                                                    clus
vv                                                   COL3A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              12
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             31
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   COL3A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              263
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    18
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V10, binary
                  cls
clus                 0   1
  COL3A1 MUTATED     3  50
  COL3A1 WILD-TYPE  17 410
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED      3   50
  COL3A1 WILD-TYPE   17  410
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO               3               17
  YES             50              410
[1] 2 2
[1] FALSE
D151V11, continuous
D151V12, continuous
                  vv
clus                R0  R1  R2  RX
  COL3A1 MUTATED    33   2   0   1
  COL3A1 WILD-TYPE 277   9   4  24
D151V13, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  R0             33              277
  R1              2                9
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL3A1 MUTATED                                  0     0
  COL3A1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL3A1 MUTATED                           4    45
  COL3A1 WILD-TYPE                        25   332
D151V14, multiclass
                                  clus
vv                                 COL3A1 MUTATED COL3A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     4               25
  WHITE                                        45              332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V15, binary
                  cls
clus                 0   1
  COL3A1 MUTATED     3  38
  COL3A1 WILD-TYPE   3 311
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED      3   38
  COL3A1 WILD-TYPE    3  311
                        clus
vv                       COL3A1 MUTATED COL3A1 WILD-TYPE
  HISPANIC OR LATINO                  3                3
  NOT HISPANIC OR LATINO             38              311
[1] 2 2
[1] FALSE

Clustering(152) Variable = RBBP6 MUTATION ANALYSIS
D152V1, survival
                 sevent
clus2               0   1
  RBBP6 MUTATED    11   6
  RBBP6 WILD-TYPE 304 135
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             17             439 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              6             135 
$`RBBP6 MUTATED`
TCGA-05-4397 TCGA-44-2656 TCGA-44-3918 TCGA-44-7660 TCGA-44-8119 TCGA-44-A479 
       24.03        46.98        34.06        19.46         3.25        15.98 
TCGA-49-4486 TCGA-49-4505 TCGA-49-6742 TCGA-50-5066 TCGA-50-5941 TCGA-53-7624 
       76.21        14.07        14.63        31.04        18.64        34.29 
TCGA-55-8092 TCGA-55-A490 TCGA-64-1681 TCGA-86-7955 TCGA-86-A4JF 
        5.06         1.58        38.37        16.70        17.62 

$`RBBP6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       14.60        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
       17.59        23.64        12.66         8.55        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 
       11.08        11.54        13.64        13.45        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        46.72        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
       21.47         8.45        15.12        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.66        19.73         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        20.65        55.43        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  RBBP6 MUTATED RBBP6 WILD-TYPE 
           1.58            0.00 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
          76.21          223.96 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
          18.64           17.98 
[1] "1.6 - 76.2 (18.6)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D152V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RBBP6 MUTATED         0        3        5         1         6          1
  RBBP6 WILD-TYPE       4      120      128        45        61         69
                 vv
clus              STAGE IIIB STAGE IV
  RBBP6 MUTATED            0        1
  RBBP6 WILD-TYPE         11       24
D152V3, multiclass
            clus
vv           RBBP6 MUTATED RBBP6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               5             128
  STAGE IIA              1              45
  STAGE IIB              6              61
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBBP6 MUTATED     3  11   3   0
  RBBP6 WILD-TYPE 152 250  40  18
D152V4, multiclass
    clus
vv   RBBP6 MUTATED RBBP6 WILD-TYPE
  T1             3             152
  T2            11             250
  T3             3              40
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  RBBP6 MUTATED    13   3     1
  RBBP6 WILD-TYPE 294  86    71
D152V5, multiclass
       clus
vv      RBBP6 MUTATED RBBP6 WILD-TYPE
  N0               13             294
  N1                3              86
  N2+N3             1              71
[1] 3 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
  RBBP6 MUTATED    12   1
  RBBP6 WILD-TYPE 315  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED     12    1
  RBBP6 WILD-TYPE  315   22
   clus
vv  RBBP6 MUTATED RBBP6 WILD-TYPE
  0            12             315
  1             1              22
[1] 2 2
[1] FALSE
D152V7, binary
                 cls
clus                0   1
  RBBP6 MUTATED     6  11
  RBBP6 WILD-TYPE 253 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      6   11
  RBBP6 WILD-TYPE  253  210
        clus
vv       RBBP6 MUTATED RBBP6 WILD-TYPE
  FEMALE             6             253
  MALE              11             210
[1] 2 2
[1] FALSE
D152V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RBBP6 MUTATED                            0                                 2
  RBBP6 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RBBP6 MUTATED                                                   14
  RBBP6 WILD-TYPE                                                280
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RBBP6 MUTATED                                            0
  RBBP6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RBBP6 MUTATED                                               0
  RBBP6 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RBBP6 MUTATED                                0
  RBBP6 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RBBP6 MUTATED                                    0
  RBBP6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RBBP6 MUTATED                              0                             0
  RBBP6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RBBP6 MUTATED                                               0
  RBBP6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RBBP6 MUTATED                              1
  RBBP6 WILD-TYPE                            8
D152V9, multiclass
                                                    clus
vv                                                   RBBP6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            14
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   RBBP6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V10, binary
                 cls
clus                0   1
  RBBP6 MUTATED     0  17
  RBBP6 WILD-TYPE  20 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      0   17
  RBBP6 WILD-TYPE   20  443
     clus
vv    RBBP6 MUTATED RBBP6 WILD-TYPE
  NO              0              20
  YES            17             443
[1] 2 2
[1] FALSE
D152V11, continuous
D152V12, continuous
                 vv
clus               R0  R1  R2  RX
  RBBP6 MUTATED    12   0   0   1
  RBBP6 WILD-TYPE 298  11   4  24
D152V13, multiclass
    clus
vv   RBBP6 MUTATED RBBP6 WILD-TYPE
  R0            12             298
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBBP6 MUTATED                                  0     0
  RBBP6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBBP6 MUTATED                           2    14
  RBBP6 WILD-TYPE                        27   363
D152V14, multiclass
                                  clus
vv                                 RBBP6 MUTATED RBBP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V15, binary
                 cls
clus                0   1
  RBBP6 MUTATED     1  14
  RBBP6 WILD-TYPE   5 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      1   14
  RBBP6 WILD-TYPE    5  335
                        clus
vv                       RBBP6 MUTATED RBBP6 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            14             335
[1] 2 2
[1] FALSE

Clustering(153) Variable = RFX1 MUTATION ANALYSIS
D153V1, survival
                sevent
clus2              0   1
  RFX1 MUTATED     9   0
  RFX1 WILD-TYPE 306 141
  RFX1 MUTATED RFX1 WILD-TYPE 
             9            447 
  RFX1 MUTATED RFX1 WILD-TYPE 
             0            141 
$`RFX1 MUTATED`
TCGA-44-3918 TCGA-44-6144 TCGA-44-A47A TCGA-55-7815 TCGA-55-8089 TCGA-67-3771 
       34.06        23.77        15.32         1.78         3.29        20.05 
TCGA-69-7974 TCGA-86-8054 TCGA-86-8073 
        6.05        24.49        24.33 

$`RFX1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        38.24         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        28.37        12.59        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 
       23.18         1.28         1.28         1.12         0.79         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        16.70         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  RFX1 MUTATED RFX1 WILD-TYPE 
          1.78           0.00 
  RFX1 MUTATED RFX1 WILD-TYPE 
         34.06         223.96 
  RFX1 MUTATED RFX1 WILD-TYPE 
         20.05          17.98 
[1] "1.8 - 34.1 (20.1)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "9200000"
D153V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RFX1 MUTATED         0        4        3         0         1          1
  RFX1 WILD-TYPE       4      119      130        46        66         69
                vv
clus             STAGE IIIB STAGE IV
  RFX1 MUTATED            0        0
  RFX1 WILD-TYPE         11       25
D153V3, multiclass
            clus
vv           RFX1 MUTATED RFX1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RFX1 MUTATED     4   5   0   0
  RFX1 WILD-TYPE 151 256  43  18
D153V4, multiclass
    clus
vv   RFX1 MUTATED RFX1 WILD-TYPE
  T1            4            151
  T2            5            256
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  RFX1 MUTATED     7   1     1
  RFX1 WILD-TYPE 300  88    71
D153V5, multiclass
       clus
vv      RFX1 MUTATED RFX1 WILD-TYPE
  N0               7            300
  N1               1             88
  N2+N3            1             71
[1] 3 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
  RFX1 MUTATED     6   0
  RFX1 WILD-TYPE 321  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      6    0
  RFX1 WILD-TYPE  321   23
   clus
vv  RFX1 MUTATED RFX1 WILD-TYPE
  0            6            321
  1            0             23
[1] 2 2
[1] FALSE
D153V7, binary
                cls
clus               0   1
  RFX1 MUTATED     4   5
  RFX1 WILD-TYPE 255 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      4    5
  RFX1 WILD-TYPE  255  216
        clus
vv       RFX1 MUTATED RFX1 WILD-TYPE
  FEMALE            4            255
  MALE              5            216
[1] 2 2
[1] FALSE
D153V8, continuous
[1] "Remove cluster labels:" "RFX1 MUTATED"          
clus
  RFX1 MUTATED RFX1 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-69-8254     TCGA-71-6725     TCGA-71-8520     TCGA-73-4659 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4676 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8055     TCGA-86-8056 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"RFX1 WILD-TYPE" "RFX1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RFX1 MUTATED                            1                                 1
  RFX1 WILD-TYPE                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RFX1 MUTATED                                                    6
  RFX1 WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RFX1 MUTATED                                            0
  RFX1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RFX1 MUTATED                                               1
  RFX1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RFX1 MUTATED                                0
  RFX1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RFX1 MUTATED                                    0
  RFX1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RFX1 MUTATED                              0                             0
  RFX1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RFX1 MUTATED                                               0
  RFX1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RFX1 MUTATED                              0
  RFX1 WILD-TYPE                            9
D153V9, multiclass
                                                    clus
vv                                                   RFX1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RFX1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V10, binary
                cls
clus               0   1
  RFX1 MUTATED     1   8
  RFX1 WILD-TYPE  19 452
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      1    8
  RFX1 WILD-TYPE   19  452
     clus
vv    RFX1 MUTATED RFX1 WILD-TYPE
  NO             1             19
  YES            8            452
[1] 2 2
[1] FALSE
D153V11, continuous
D153V12, continuous
                vv
clus              R0  R1  R2  RX
  RFX1 MUTATED     7   0   0   1
  RFX1 WILD-TYPE 303  11   4  24
D153V13, multiclass
    clus
vv   RFX1 MUTATED RFX1 WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RFX1 MUTATED                                  0     0
  RFX1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RFX1 MUTATED                           1     7
  RFX1 WILD-TYPE                        28   370
D153V14, multiclass
                                  clus
vv                                 RFX1 MUTATED RFX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V15, binary
                cls
clus               0   1
  RFX1 MUTATED     0   8
  RFX1 WILD-TYPE   6 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      0    8
  RFX1 WILD-TYPE    6  341
                        clus
vv                       RFX1 MUTATED RFX1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(154) Variable = PRB2 MUTATION ANALYSIS
D154V1, survival
                sevent
clus2              0   1
  PRB2 MUTATED     7   6
  PRB2 WILD-TYPE 308 135
  PRB2 MUTATED PRB2 WILD-TYPE 
            13            443 
  PRB2 MUTATED PRB2 WILD-TYPE 
             6            135 
$`PRB2 MUTATED`
TCGA-44-A47F TCGA-53-7624 TCGA-55-7907 TCGA-55-7911 TCGA-55-8092 TCGA-55-8512 
       11.08        34.29         0.53        17.65         5.06         0.10 
TCGA-55-A490 TCGA-62-A46R TCGA-86-8359 TCGA-91-6848 TCGA-93-A4JO TCGA-MP-A4T4 
        1.58        56.71        14.60         7.36         1.08        86.04 
TCGA-NJ-A55O 
        0.43 

$`PRB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 
        1.78         1.45        18.64         6.48         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.30         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        21.47         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
        6.12        23.61        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26        19.82        59.11 

  PRB2 MUTATED PRB2 WILD-TYPE 
           0.1            0.0 
  PRB2 MUTATED PRB2 WILD-TYPE 
         86.04         223.96 
  PRB2 MUTATED PRB2 WILD-TYPE 
          7.36          18.64 
[1] "0.1 - 86.0 (7.4)"   "0.0 - 224.0 (18.6)"
[1] "hr=" "1.8"
D154V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PRB2 MUTATED         0        2        1         3         3          2
  PRB2 WILD-TYPE       4      121      132        43        64         68
                vv
clus             STAGE IIIB STAGE IV
  PRB2 MUTATED            0        2
  PRB2 WILD-TYPE         11       23
D154V3, multiclass
            clus
vv           PRB2 MUTATED PRB2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              1            132
  STAGE IIA             3             43
  STAGE IIB             3             64
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PRB2 MUTATED     4   7   2   0
  PRB2 WILD-TYPE 151 254  41  18
D154V4, multiclass
    clus
vv   PRB2 MUTATED PRB2 WILD-TYPE
  T1            4            151
  T2            7            254
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  PRB2 MUTATED     6   5     2
  PRB2 WILD-TYPE 301  84    70
D154V5, multiclass
       clus
vv      PRB2 MUTATED PRB2 WILD-TYPE
  N0               6            301
  N1               5             84
  N2+N3            2             70
[1] 3 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
  PRB2 MUTATED     5   2
  PRB2 WILD-TYPE 322  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      5    2
  PRB2 WILD-TYPE  322   21
   clus
vv  PRB2 MUTATED PRB2 WILD-TYPE
  0            5            322
  1            2             21
[1] 2 2
[1] FALSE
D154V7, binary
                cls
clus               0   1
  PRB2 MUTATED     5   8
  PRB2 WILD-TYPE 254 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      5    8
  PRB2 WILD-TYPE  254  213
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  FEMALE            5            254
  MALE              8            213
[1] 2 2
[1] FALSE
D154V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PRB2 MUTATED                            0                                 2
  PRB2 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PRB2 MUTATED                                                    9
  PRB2 WILD-TYPE                                                285
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PRB2 MUTATED                                            0
  PRB2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PRB2 MUTATED                                               1
  PRB2 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  PRB2 MUTATED                                0
  PRB2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  PRB2 MUTATED                                    0
  PRB2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PRB2 MUTATED                              0                             0
  PRB2 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PRB2 MUTATED                                               0
  PRB2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  PRB2 MUTATED                              1
  PRB2 WILD-TYPE                            8
D154V9, multiclass
                                                    clus
vv                                                   PRB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   PRB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V10, binary
                cls
clus               0   1
  PRB2 MUTATED     0  13
  PRB2 WILD-TYPE  20 447
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      0   13
  PRB2 WILD-TYPE   20  447
     clus
vv    PRB2 MUTATED PRB2 WILD-TYPE
  NO             0             20
  YES           13            447
[1] 2 2
[1] FALSE
D154V11, continuous
D154V12, continuous
                vv
clus              R0  R1  R2  RX
  PRB2 MUTATED     9   0   0   1
  PRB2 WILD-TYPE 301  11   4  24
D154V13, multiclass
    clus
vv   PRB2 MUTATED PRB2 WILD-TYPE
  R0            9            301
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRB2 MUTATED                                  0     0
  PRB2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PRB2 MUTATED                           0    13
  PRB2 WILD-TYPE                        29   364
D154V14, multiclass
                                  clus
vv                                 PRB2 MUTATED PRB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                      13            364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V15, binary
                cls
clus               0   1
  PRB2 MUTATED     1  11
  PRB2 WILD-TYPE   5 338
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      1   11
  PRB2 WILD-TYPE    5  338
                        clus
vv                       PRB2 MUTATED PRB2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           11            338
[1] 2 2
[1] FALSE

Clustering(155) Variable = COL25A1 MUTATION ANALYSIS
D155V1, survival
                   sevent
clus2                 0   1
  COL25A1 MUTATED    24   5
  COL25A1 WILD-TYPE 291 136
  COL25A1 MUTATED COL25A1 WILD-TYPE 
               29               427 
  COL25A1 MUTATED COL25A1 WILD-TYPE 
                5               136 
$`COL25A1 MUTATED`
TCGA-05-4382 TCGA-05-5715 TCGA-38-4631 TCGA-44-2656 TCGA-44-2665 TCGA-44-3398 
       19.96         2.04        11.64        46.98        42.77        38.24 
TCGA-44-5644 TCGA-49-6767 TCGA-50-5930 TCGA-50-8460 TCGA-55-1595 TCGA-55-6985 
       28.37        22.26         9.27        27.25        48.62        40.54 
TCGA-55-7570 TCGA-55-7907 TCGA-55-8301 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
        0.20         0.53         1.45         0.26        17.72         0.30 
TCGA-78-7166 TCGA-78-7220 TCGA-86-6851 TCGA-86-8358 TCGA-91-8499 TCGA-95-A4VP 
        8.48        26.53         5.88        21.47         1.18        19.89 
TCGA-97-7554 TCGA-97-7937 TCGA-99-8028 TCGA-99-8033 TCGA-MP-A4TK 
       25.48         5.95        36.76         5.59        19.13 

$`COL25A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 
        4.37        13.15        24.36        37.15        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         8.22        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        34.29        30.54        13.94         9.21        23.05 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
        2.20        45.34        32.71        60.03        24.99       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
       70.26         1.74         0.59         1.15         7.99         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
        0.76         0.95         0.36         0.49         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
       22.29         7.07       104.19       223.96        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       14.27         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        18.18        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       43.79         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-J2-8192 
       18.67        20.68        24.56        34.85         1.45        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        14.10        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  COL25A1 MUTATED COL25A1 WILD-TYPE 
              0.2               0.0 
  COL25A1 MUTATED COL25A1 WILD-TYPE 
            48.62            223.96 
  COL25A1 MUTATED COL25A1 WILD-TYPE 
            19.13             17.98 
[1] "0.2 - 48.6 (19.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.4"
D155V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL25A1 MUTATED         0        7       13         2         4          5
  COL25A1 WILD-TYPE       4      116      120        44        63         65
                   vv
clus                STAGE IIIB STAGE IV
  COL25A1 MUTATED            0        1
  COL25A1 WILD-TYPE         11       24
D155V3, multiclass
            clus
vv           COL25A1 MUTATED COL25A1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 7               116
  STAGE IB                13               120
  STAGE IIA                2                44
  STAGE IIB                4                63
  STAGE IIIA               5                65
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL25A1 MUTATED     8  21   2   0
  COL25A1 WILD-TYPE 147 240  41  18
D155V4, multiclass
    clus
vv   COL25A1 MUTATED COL25A1 WILD-TYPE
  T1               8               147
  T2              21               240
  T3               2                41
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  COL25A1 MUTATED    21   5     5
  COL25A1 WILD-TYPE 286  84    67
D155V5, multiclass
       clus
vv      COL25A1 MUTATED COL25A1 WILD-TYPE
  N0                 21               286
  N1                  5                84
  N2+N3               5                67
[1] 3 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
  COL25A1 MUTATED    19   1
  COL25A1 WILD-TYPE 308  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL25A1 MUTATED     19    1
  COL25A1 WILD-TYPE  308   22
   clus
vv  COL25A1 MUTATED COL25A1 WILD-TYPE
  0              19               308
  1               1                22
[1] 2 2
[1] FALSE
D155V7, binary
                   cls
clus                  0   1
  COL25A1 MUTATED    19  13
  COL25A1 WILD-TYPE 240 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL25A1 MUTATED     19   13
  COL25A1 WILD-TYPE  240  208
        clus
vv       COL25A1 MUTATED COL25A1 WILD-TYPE
  FEMALE              19               240
  MALE                13               208
[1] 2 2
[1] FALSE
D155V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  COL25A1 MUTATED                            1
  COL25A1 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL25A1 MUTATED                                   6
  COL25A1 WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL25A1 MUTATED                                                   19
  COL25A1 WILD-TYPE                                                275
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL25A1 MUTATED                                            0
  COL25A1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL25A1 MUTATED                                               0
  COL25A1 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  COL25A1 MUTATED                                1
  COL25A1 WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  COL25A1 MUTATED                                    1
  COL25A1 WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL25A1 MUTATED                              0                             3
  COL25A1 WILD-TYPE                            2                            19
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL25A1 MUTATED                                               1
  COL25A1 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  COL25A1 MUTATED                              0
  COL25A1 WILD-TYPE                            9
D155V9, multiclass
                                                    clus
vv                                                   COL25A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   COL25A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               275
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     19
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V10, binary
                   cls
clus                  0   1
  COL25A1 MUTATED     3  29
  COL25A1 WILD-TYPE  17 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL25A1 MUTATED      3   29
  COL25A1 WILD-TYPE   17  431
     clus
vv    COL25A1 MUTATED COL25A1 WILD-TYPE
  NO                3                17
  YES              29               431
[1] 2 2
[1] FALSE
D155V11, continuous
D155V12, continuous
                   vv
clus                 R0  R1  R2  RX
  COL25A1 MUTATED    22   0   1   1
  COL25A1 WILD-TYPE 288  11   3  24
D155V13, multiclass
    clus
vv   COL25A1 MUTATED COL25A1 WILD-TYPE
  R0              22               288
  R1               0                11
  R2               1                 3
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL25A1 MUTATED                                  0     1
  COL25A1 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COL25A1 MUTATED                           2    23
  COL25A1 WILD-TYPE                        27   354
D155V14, multiclass
                                  clus
vv                                 COL25A1 MUTATED COL25A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         23               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V15, binary
                   cls
clus                  0   1
  COL25A1 MUTATED     0  21
  COL25A1 WILD-TYPE   6 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL25A1 MUTATED      0   21
  COL25A1 WILD-TYPE    6  328
                        clus
vv                       COL25A1 MUTATED COL25A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              21               328
[1] 2 2
[1] FALSE

Clustering(156) Variable = PPP2R5B MUTATION ANALYSIS
D156V1, survival
                   sevent
clus2                 0   1
  PPP2R5B MUTATED     3   4
  PPP2R5B WILD-TYPE 312 137
  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
                7               449 
  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
                4               137 
$`PPP2R5B MUTATED`
TCGA-05-4382 TCGA-44-7671 TCGA-55-7728 TCGA-55-7914 TCGA-78-7155 TCGA-86-7714 
       19.96        17.59         0.79         6.15        38.50        20.55 
TCGA-91-6829 
       41.36 

$`PPP2R5B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        29.00        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 
        1.32        23.18         1.28         1.28         1.12         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
        1.45        18.64         0.53         6.48        17.65        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        13.87        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
       13.32        17.62        13.64        26.47        10.62         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
             0.79              0.00 
  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
            41.36            223.96 
  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
            19.96             17.98 
[1] "0.8 - 41.4 (20.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.2"
D156V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PPP2R5B MUTATED         0        0        5         1         0          1
  PPP2R5B WILD-TYPE       4      123      128        45        67         69
                   vv
clus                STAGE IIIB STAGE IV
  PPP2R5B MUTATED            0        0
  PPP2R5B WILD-TYPE         11       25
D156V3, multiclass
            clus
vv           PPP2R5B MUTATED PPP2R5B WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0               123
  STAGE IB                 5               128
  STAGE IIA                1                45
  STAGE IIB                0                67
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP2R5B MUTATED     2   5   0   0
  PPP2R5B WILD-TYPE 153 256  43  18
D156V4, multiclass
    clus
vv   PPP2R5B MUTATED PPP2R5B WILD-TYPE
  T1               2               153
  T2               5               256
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  PPP2R5B MUTATED     5   1     1
  PPP2R5B WILD-TYPE 302  88    71
D156V5, multiclass
       clus
vv      PPP2R5B MUTATED PPP2R5B WILD-TYPE
  N0                  5               302
  N1                  1                88
  N2+N3               1                71
[1] 3 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
  PPP2R5B MUTATED     4   0
  PPP2R5B WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5B MUTATED      4    0
  PPP2R5B WILD-TYPE  323   23
   clus
vv  PPP2R5B MUTATED PPP2R5B WILD-TYPE
  0               4               323
  1               0                23
[1] 2 2
[1] FALSE
D156V7, binary
                   cls
clus                  0   1
  PPP2R5B MUTATED     3   4
  PPP2R5B WILD-TYPE 256 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5B MUTATED      3    4
  PPP2R5B WILD-TYPE  256  217
        clus
vv       PPP2R5B MUTATED PPP2R5B WILD-TYPE
  FEMALE               3               256
  MALE                 4               217
[1] 2 2
[1] FALSE
D156V8, continuous
[1] "Remove cluster labels:" "PPP2R5B MUTATED"       
clus
  PPP2R5B MUTATED PPP2R5B WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-55-8089        TCGA-55-8096        TCGA-55-8205        TCGA-55-8208 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8511        TCGA-55-8512 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-86-7954        TCGA-86-7955        TCGA-86-8055        TCGA-86-8056 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-86-8074        TCGA-86-8075        TCGA-86-8076        TCGA-86-8278 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8281        TCGA-86-8358        TCGA-86-8359 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-86-8668        TCGA-86-8669        TCGA-86-8671        TCGA-86-A4JF 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"PPP2R5B WILD-TYPE" "PPP2R5B WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PPP2R5B MUTATED                            0
  PPP2R5B WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PPP2R5B MUTATED                                   3
  PPP2R5B WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PPP2R5B MUTATED                                                    2
  PPP2R5B WILD-TYPE                                                292
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PPP2R5B MUTATED                                            0
  PPP2R5B WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PPP2R5B MUTATED                                               1
  PPP2R5B WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  PPP2R5B MUTATED                                0
  PPP2R5B WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  PPP2R5B MUTATED                                    0
  PPP2R5B WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PPP2R5B MUTATED                              0                             0
  PPP2R5B WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PPP2R5B MUTATED                                               0
  PPP2R5B WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  PPP2R5B MUTATED                              1
  PPP2R5B WILD-TYPE                            8
D156V9, multiclass
                                                    clus
vv                                                   PPP2R5B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   PPP2R5B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V10, binary
                   cls
clus                  0   1
  PPP2R5B MUTATED     0   7
  PPP2R5B WILD-TYPE  20 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5B MUTATED      0    7
  PPP2R5B WILD-TYPE   20  453
     clus
vv    PPP2R5B MUTATED PPP2R5B WILD-TYPE
  NO                0                20
  YES               7               453
[1] 2 2
[1] FALSE
D156V11, continuous
D156V12, continuous
                   vv
clus                 R0  R1  R2  RX
  PPP2R5B MUTATED     6   0   0   0
  PPP2R5B WILD-TYPE 304  11   4  25
D156V13, multiclass
    clus
vv   PPP2R5B MUTATED PPP2R5B WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R5B MUTATED                                  0     0
  PPP2R5B WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R5B MUTATED                           2     3
  PPP2R5B WILD-TYPE                        27   374
D156V14, multiclass
                                  clus
vv                                 PPP2R5B MUTATED PPP2R5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                          3               374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V15, binary
                   cls
clus                  0   1
  PPP2R5B MUTATED     0   4
  PPP2R5B WILD-TYPE   6 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5B MUTATED      0    4
  PPP2R5B WILD-TYPE    6  345
                        clus
vv                       PPP2R5B MUTATED PPP2R5B WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               4               345
[1] 2 2
[1] FALSE

Clustering(157) Variable = DZIP1L MUTATION ANALYSIS
D157V1, survival
                  sevent
clus2                0   1
  DZIP1L MUTATED     8   3
  DZIP1L WILD-TYPE 307 138
  DZIP1L MUTATED DZIP1L WILD-TYPE 
              11              445 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
               3              138 
$`DZIP1L MUTATED`
TCGA-44-A479 TCGA-49-4514 TCGA-50-5049 TCGA-55-6969 TCGA-64-5775 TCGA-86-8054 
       15.98        55.89        70.55        40.73         2.04        24.49 
TCGA-86-8673 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-O1-A52J 
       14.96         6.12         1.12         2.86        59.11 

$`DZIP1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25         8.55        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.46        29.75        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       20.65        55.43        38.37        87.98        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82         9.76         4.18        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       17.29         1.22        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R 
       19.82 

  DZIP1L MUTATED DZIP1L WILD-TYPE 
            1.12             0.00 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
           70.55           223.96 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
           15.98            18.08 
[1] "1.1 - 70.5 (16.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.5"
D157V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DZIP1L MUTATED         0        3        4         1         2          1
  DZIP1L WILD-TYPE       4      120      129        45        65         69
                  vv
clus               STAGE IIIB STAGE IV
  DZIP1L MUTATED            0        0
  DZIP1L WILD-TYPE         11       25
D157V3, multiclass
            clus
vv           DZIP1L MUTATED DZIP1L WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                4              129
  STAGE IIA               1               45
  STAGE IIB               2               65
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DZIP1L MUTATED     2   7   1   1
  DZIP1L WILD-TYPE 153 254  42  17
D157V4, multiclass
    clus
vv   DZIP1L MUTATED DZIP1L WILD-TYPE
  T1              2              153
  T2              7              254
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  DZIP1L MUTATED     9   2     0
  DZIP1L WILD-TYPE 298  87    72
D157V5, multiclass
       clus
vv      DZIP1L MUTATED DZIP1L WILD-TYPE
  N0                 9              298
  N1                 2               87
  N2+N3              0               72
[1] 3 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
  DZIP1L MUTATED     7   0
  DZIP1L WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED      7    0
  DZIP1L WILD-TYPE  320   23
   clus
vv  DZIP1L MUTATED DZIP1L WILD-TYPE
  0              7              320
  1              0               23
[1] 2 2
[1] FALSE
D157V7, binary
                  cls
clus                 0   1
  DZIP1L MUTATED     4   7
  DZIP1L WILD-TYPE 255 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED      4    7
  DZIP1L WILD-TYPE  255  214
        clus
vv       DZIP1L MUTATED DZIP1L WILD-TYPE
  FEMALE              4              255
  MALE                7              214
[1] 2 2
[1] FALSE
D157V8, continuous
[1] "Remove cluster labels:" "DZIP1L MUTATED"        
clus
  DZIP1L MUTATED DZIP1L WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8279       TCGA-86-8281 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8669 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-86-8671       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-93-7348       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" "DZIP1L WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DZIP1L MUTATED                            1                                 1
  DZIP1L WILD-TYPE                         17                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DZIP1L MUTATED                                                    7
  DZIP1L WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DZIP1L MUTATED                                            0
  DZIP1L WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DZIP1L MUTATED                                               1
  DZIP1L WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  DZIP1L MUTATED                                0
  DZIP1L WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  DZIP1L MUTATED                                    0
  DZIP1L WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DZIP1L MUTATED                              0                             1
  DZIP1L WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DZIP1L MUTATED                                               0
  DZIP1L WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  DZIP1L MUTATED                              0
  DZIP1L WILD-TYPE                            9
D157V9, multiclass
                                                    clus
vv                                                   DZIP1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   DZIP1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V10, binary
                  cls
clus                 0   1
  DZIP1L MUTATED     1  10
  DZIP1L WILD-TYPE  19 450
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED      1   10
  DZIP1L WILD-TYPE   19  450
     clus
vv    DZIP1L MUTATED DZIP1L WILD-TYPE
  NO               1               19
  YES             10              450
[1] 2 2
[1] FALSE
D157V11, continuous
D157V12, continuous
                  vv
clus                R0  R1  R2  RX
  DZIP1L MUTATED     5   0   0   2
  DZIP1L WILD-TYPE 305  11   4  23
D157V13, multiclass
    clus
vv   DZIP1L MUTATED DZIP1L WILD-TYPE
  R0              5              305
  R1              0               11
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DZIP1L MUTATED                                  0     1
  DZIP1L WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DZIP1L MUTATED                           2     8
  DZIP1L WILD-TYPE                        27   369
D157V14, multiclass
                                  clus
vv                                 DZIP1L MUTATED DZIP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                         8              369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V15, binary
                  cls
clus                 0   1
  DZIP1L MUTATED     0   9
  DZIP1L WILD-TYPE   6 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED      0    9
  DZIP1L WILD-TYPE    6  340
                        clus
vv                       DZIP1L MUTATED DZIP1L WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              9              340
[1] 2 2
[1] FALSE

Clustering(158) Variable = RLTPR MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2               0   1
  RLTPR MUTATED    13   1
  RLTPR WILD-TYPE 302 140
  RLTPR MUTATED RLTPR WILD-TYPE 
             14             442 
  RLTPR MUTATED RLTPR WILD-TYPE 
              1             140 
$`RLTPR MUTATED`
TCGA-05-4430 TCGA-05-5423 TCGA-44-2656 TCGA-44-3918 TCGA-44-8117 TCGA-44-8120 
       25.02         4.96        46.98        34.06        12.66         8.55 
TCGA-53-7624 TCGA-55-8089 TCGA-55-8514 TCGA-55-A48Y TCGA-64-5815 TCGA-86-8673 
       34.29         3.29         6.64        20.71        28.47        14.96 
TCGA-95-A4VK TCGA-99-7458 
       21.40        24.56 

$`RLTPR WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       17.59        23.64         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        25.61         7.59        27.25        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
       17.72         0.30         0.10         4.80        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        22.65        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
        1.15        13.91        30.84        27.58         0.62        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  RLTPR MUTATED RLTPR WILD-TYPE 
           3.29            0.00 
  RLTPR MUTATED RLTPR WILD-TYPE 
          46.98          223.96 
  RLTPR MUTATED RLTPR WILD-TYPE 
         21.055          17.950 
[1] "3.3 - 47.0 (21.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "3.6"
D158V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RLTPR MUTATED         0        2        6         1         3          2
  RLTPR WILD-TYPE       4      121      127        45        64         68
                 vv
clus              STAGE IIIB STAGE IV
  RLTPR MUTATED            0        1
  RLTPR WILD-TYPE         11       24
D158V3, multiclass
            clus
vv           RLTPR MUTATED RLTPR WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               6             127
  STAGE IIA              1              45
  STAGE IIB              3              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RLTPR MUTATED     2  12   0   1
  RLTPR WILD-TYPE 153 249  43  17
D158V4, multiclass
    clus
vv   RLTPR MUTATED RLTPR WILD-TYPE
  T1             2             153
  T2            12             249
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  RLTPR MUTATED    11   3     1
  RLTPR WILD-TYPE 296  86    71
D158V5, multiclass
       clus
vv      RLTPR MUTATED RLTPR WILD-TYPE
  N0               11             296
  N1                3              86
  N2+N3             1              71
[1] 3 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
  RLTPR MUTATED    13   1
  RLTPR WILD-TYPE 314  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RLTPR MUTATED     13    1
  RLTPR WILD-TYPE  314   22
   clus
vv  RLTPR MUTATED RLTPR WILD-TYPE
  0            13             314
  1             1              22
[1] 2 2
[1] FALSE
D158V7, binary
                 cls
clus                0   1
  RLTPR MUTATED     7   8
  RLTPR WILD-TYPE 252 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RLTPR MUTATED      7    8
  RLTPR WILD-TYPE  252  213
        clus
vv       RLTPR MUTATED RLTPR WILD-TYPE
  FEMALE             7             252
  MALE               8             213
[1] 2 2
[1] FALSE
D158V8, continuous
[1] "Remove cluster labels:" "RLTPR MUTATED"         
clus
  RLTPR MUTATED RLTPR WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-MN-A4N1 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"RLTPR WILD-TYPE" "RLTPR WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RLTPR MUTATED                            0                                 4
  RLTPR WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RLTPR MUTATED                                                    9
  RLTPR WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RLTPR MUTATED                                            0
  RLTPR WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RLTPR MUTATED                                               2
  RLTPR WILD-TYPE                                            17
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RLTPR MUTATED                                0
  RLTPR WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RLTPR MUTATED                                    0
  RLTPR WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RLTPR MUTATED                              0                             0
  RLTPR WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RLTPR MUTATED                                               0
  RLTPR WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RLTPR MUTATED                              0
  RLTPR WILD-TYPE                            9
D158V9, multiclass
                                                    clus
vv                                                   RLTPR MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  2
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   RLTPR WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   17
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V10, binary
                 cls
clus                0   1
  RLTPR MUTATED     0  15
  RLTPR WILD-TYPE  20 445
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RLTPR MUTATED      0   15
  RLTPR WILD-TYPE   20  445
     clus
vv    RLTPR MUTATED RLTPR WILD-TYPE
  NO              0              20
  YES            15             445
[1] 2 2
[1] FALSE
D158V11, continuous
D158V12, continuous
                 vv
clus               R0  R1  R2  RX
  RLTPR MUTATED    11   0   0   1
  RLTPR WILD-TYPE 299  11   4  24
D158V13, multiclass
    clus
vv   RLTPR MUTATED RLTPR WILD-TYPE
  R0            11             299
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RLTPR MUTATED                                  0     0
  RLTPR WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RLTPR MUTATED                           2    10
  RLTPR WILD-TYPE                        27   367
D158V14, multiclass
                                  clus
vv                                 RLTPR MUTATED RLTPR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V15, binary
                 cls
clus                0   1
  RLTPR MUTATED     1  11
  RLTPR WILD-TYPE   5 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RLTPR MUTATED      1   11
  RLTPR WILD-TYPE    5  338
                        clus
vv                       RLTPR MUTATED RLTPR WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            11             338
[1] 2 2
[1] FALSE

Clustering(159) Variable = CD40LG MUTATION ANALYSIS
D159V1, survival
                  sevent
clus2                0   1
  CD40LG MUTATED     5   0
  CD40LG WILD-TYPE 310 141
  CD40LG MUTATED CD40LG WILD-TYPE 
               5              451 
  CD40LG MUTATED CD40LG WILD-TYPE 
               0              141 
$`CD40LG MUTATED`
TCGA-44-8120 TCGA-55-7995 TCGA-64-1676 TCGA-86-8671 TCGA-99-7458 
        8.55         0.16        56.81        27.58        24.56 

$`CD40LG WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 
       21.47        14.60         1.15        13.91        30.84         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CD40LG MUTATED CD40LG WILD-TYPE 
            0.16             0.00 
  CD40LG MUTATED CD40LG WILD-TYPE 
           56.81           223.96 
  CD40LG MUTATED CD40LG WILD-TYPE 
           24.56            17.98 
[1] "0.2 - 56.8 (24.6)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "9100000"
D159V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CD40LG MUTATED         0        2        2         0         1          1
  CD40LG WILD-TYPE       4      121      131        46        66         69
                  vv
clus               STAGE IIIB STAGE IV
  CD40LG MUTATED            0        0
  CD40LG WILD-TYPE         11       25
D159V3, multiclass
            clus
vv           CD40LG MUTATED CD40LG WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                2              131
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CD40LG MUTATED     2   3   0   1
  CD40LG WILD-TYPE 153 258  43  17
D159V4, multiclass
    clus
vv   CD40LG MUTATED CD40LG WILD-TYPE
  T1              2              153
  T2              3              258
  T3              0               43
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  CD40LG MUTATED     5   1     0
  CD40LG WILD-TYPE 302  88    72
D159V5, multiclass
       clus
vv      CD40LG MUTATED CD40LG WILD-TYPE
  N0                 5              302
  N1                 1               88
  N2+N3              0               72
[1] 3 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
  CD40LG MUTATED     6   0
  CD40LG WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD40LG MUTATED      6    0
  CD40LG WILD-TYPE  321   23
   clus
vv  CD40LG MUTATED CD40LG WILD-TYPE
  0              6              321
  1              0               23
[1] 2 2
[1] FALSE
D159V7, binary
                  cls
clus                 0   1
  CD40LG MUTATED     3   3
  CD40LG WILD-TYPE 256 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD40LG MUTATED      3    3
  CD40LG WILD-TYPE  256  218
        clus
vv       CD40LG MUTATED CD40LG WILD-TYPE
  FEMALE              3              256
  MALE                3              218
[1] 2 2
[1] FALSE
D159V8, continuous
[1] "Remove cluster labels:" "CD40LG MUTATED"        
clus
  CD40LG MUTATED CD40LG WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8279       TCGA-86-8281 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8669 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-MN-A4N1 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"CD40LG WILD-TYPE" "CD40LG WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CD40LG MUTATED                            0                                 1
  CD40LG WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CD40LG MUTATED                                                    3
  CD40LG WILD-TYPE                                                291
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CD40LG MUTATED                                            0
  CD40LG WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CD40LG MUTATED                                               1
  CD40LG WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CD40LG MUTATED                                0
  CD40LG WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CD40LG MUTATED                                    0
  CD40LG WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CD40LG MUTATED                              0                             1
  CD40LG WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CD40LG MUTATED                                               0
  CD40LG WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CD40LG MUTATED                              0
  CD40LG WILD-TYPE                            9
D159V9, multiclass
                                                    clus
vv                                                   CD40LG MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CD40LG WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V10, binary
                  cls
clus                 0   1
  CD40LG MUTATED     0   6
  CD40LG WILD-TYPE  20 454
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD40LG MUTATED      0    6
  CD40LG WILD-TYPE   20  454
     clus
vv    CD40LG MUTATED CD40LG WILD-TYPE
  NO               0               20
  YES              6              454
[1] 2 2
[1] FALSE
D159V11, continuous
D159V12, continuous
                  vv
clus                R0  R1  R2  RX
  CD40LG MUTATED     4   0   0   1
  CD40LG WILD-TYPE 306  11   4  24
D159V13, multiclass
    clus
vv   CD40LG MUTATED CD40LG WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD40LG MUTATED                                  0     0
  CD40LG WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CD40LG MUTATED                           1     4
  CD40LG WILD-TYPE                        28   373
D159V14, multiclass
                                  clus
vv                                 CD40LG MUTATED CD40LG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         4              373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V15, binary
                  cls
clus                 0   1
  CD40LG MUTATED     0   5
  CD40LG WILD-TYPE   6 344
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD40LG MUTATED      0    5
  CD40LG WILD-TYPE    6  344
                        clus
vv                       CD40LG MUTATED CD40LG WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              344
[1] 2 2
[1] FALSE

Clustering(160) Variable = LGALS2 MUTATION ANALYSIS
D160V1, survival
                  sevent
clus2                0   1
  LGALS2 MUTATED     2   3
  LGALS2 WILD-TYPE 313 138
  LGALS2 MUTATED LGALS2 WILD-TYPE 
               5              451 
  LGALS2 MUTATED LGALS2 WILD-TYPE 
               3              138 
$`LGALS2 MUTATED`
TCGA-44-7661 TCGA-55-1592 TCGA-64-5775 TCGA-78-7158 TCGA-86-8669 
       12.03        23.05         2.04         5.88        30.84 

$`LGALS2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        14.60        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94         9.21        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       32.09        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60         1.15        13.91        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  LGALS2 MUTATED LGALS2 WILD-TYPE 
            2.04             0.00 
  LGALS2 MUTATED LGALS2 WILD-TYPE 
           30.84           223.96 
  LGALS2 MUTATED LGALS2 WILD-TYPE 
           12.03            18.08 
[1] "2.0 - 30.8 (12.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "3.6"
D160V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LGALS2 MUTATED         0        2        1         0         0          1
  LGALS2 WILD-TYPE       4      121      132        46        67         69
                  vv
clus               STAGE IIIB STAGE IV
  LGALS2 MUTATED            1        0
  LGALS2 WILD-TYPE         10       25
D160V3, multiclass
            clus
vv           LGALS2 MUTATED LGALS2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                1              132
  STAGE IIA               0               46
  STAGE IIB               0               67
  STAGE IIIA              1               69
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LGALS2 MUTATED     1   2   0   2
  LGALS2 WILD-TYPE 154 259  43  16
D160V4, multiclass
    clus
vv   LGALS2 MUTATED LGALS2 WILD-TYPE
  T1              1              154
  T2              2              259
  T3              0               43
  T4              2               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"
                  vv
clus                N0  N1 N2+N3
  LGALS2 MUTATED     4   0     1
  LGALS2 WILD-TYPE 303  89    71
D160V5, multiclass
       clus
vv      LGALS2 MUTATED LGALS2 WILD-TYPE
  N0                 4              303
  N1                 0               89
  N2+N3              1               71
[1] 3 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
  LGALS2 MUTATED     5   0
  LGALS2 WILD-TYPE 322  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS2 MUTATED      5    0
  LGALS2 WILD-TYPE  322   23
   clus
vv  LGALS2 MUTATED LGALS2 WILD-TYPE
  0              5              322
  1              0               23
[1] 2 2
[1] FALSE
D160V7, binary
                  cls
clus                 0   1
  LGALS2 MUTATED     2   3
  LGALS2 WILD-TYPE 257 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS2 MUTATED      2    3
  LGALS2 WILD-TYPE  257  218
        clus
vv       LGALS2 MUTATED LGALS2 WILD-TYPE
  FEMALE              2              257
  MALE                3              218
[1] 2 2
[1] FALSE
D160V8, continuous
[1] "Remove cluster labels:" "LGALS2 MUTATED"        
clus
  LGALS2 MUTATED LGALS2 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8279       TCGA-86-8281 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8671 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" "LGALS2 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LGALS2 MUTATED                            0                                 1
  LGALS2 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LGALS2 MUTATED                                                    4
  LGALS2 WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LGALS2 MUTATED                                            0
  LGALS2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LGALS2 MUTATED                                               0
  LGALS2 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  LGALS2 MUTATED                                0
  LGALS2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  LGALS2 MUTATED                                    0
  LGALS2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LGALS2 MUTATED                              0                             0
  LGALS2 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LGALS2 MUTATED                                               0
  LGALS2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  LGALS2 MUTATED                              0
  LGALS2 WILD-TYPE                            9
D160V9, multiclass
                                                    clus
vv                                                   LGALS2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   LGALS2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V10, binary
                  cls
clus                 0   1
  LGALS2 MUTATED     0   5
  LGALS2 WILD-TYPE  20 455
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS2 MUTATED      0    5
  LGALS2 WILD-TYPE   20  455
     clus
vv    LGALS2 MUTATED LGALS2 WILD-TYPE
  NO               0               20
  YES              5              455
[1] 2 2
[1] FALSE
D160V11, continuous
D160V12, continuous
                  vv
clus                R0  R1  R2  RX
  LGALS2 MUTATED     3   1   0   0
  LGALS2 WILD-TYPE 307  10   4  25
D160V13, multiclass
    clus
vv   LGALS2 MUTATED LGALS2 WILD-TYPE
  R0              3              307
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGALS2 MUTATED                                  0     0
  LGALS2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LGALS2 MUTATED                           0     5
  LGALS2 WILD-TYPE                        29   372
D160V14, multiclass
                                  clus
vv                                 LGALS2 MUTATED LGALS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V15, binary
                  cls
clus                 0   1
  LGALS2 MUTATED     0   4
  LGALS2 WILD-TYPE   6 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS2 MUTATED      0    4
  LGALS2 WILD-TYPE    6  345
                        clus
vv                       LGALS2 MUTATED LGALS2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(161) Variable = PADI2 MUTATION ANALYSIS
D161V1, survival
                 sevent
clus2               0   1
  PADI2 MUTATED     8   1
  PADI2 WILD-TYPE 307 140
  PADI2 MUTATED PADI2 WILD-TYPE 
              9             447 
  PADI2 MUTATED PADI2 WILD-TYPE 
              1             140 
$`PADI2 MUTATED`
TCGA-44-6145 TCGA-55-8207 TCGA-55-A493 TCGA-55-A4DG TCGA-67-3771 TCGA-78-7536 
       10.78         2.17         0.92        19.99        20.05         8.02 
TCGA-86-7701 TCGA-97-8175 TCGA-99-8032 
       31.13        18.12         1.45 

$`PADI2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 
       26.56        33.30        28.37        12.59        23.77         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.08         1.51        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
       20.71        21.40         1.58        20.58        19.59        15.81 
TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       20.19         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53        31.20        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36         5.88        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        5.39        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 
       18.67        20.68        24.56        34.85        36.76         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  PADI2 MUTATED PADI2 WILD-TYPE 
           0.92            0.00 
  PADI2 MUTATED PADI2 WILD-TYPE 
          31.13          223.96 
  PADI2 MUTATED PADI2 WILD-TYPE 
          10.78           18.08 
[1] "0.9 - 31.1 (10.8)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D161V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PADI2 MUTATED         0        4        4         0         0          1
  PADI2 WILD-TYPE       4      119      129        46        67         69
                 vv
clus              STAGE IIIB STAGE IV
  PADI2 MUTATED            0        1
  PADI2 WILD-TYPE         11       24
D161V3, multiclass
            clus
vv           PADI2 MUTATED PADI2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PADI2 MUTATED     4   6   0   0
  PADI2 WILD-TYPE 151 255  43  18
D161V4, multiclass
    clus
vv   PADI2 MUTATED PADI2 WILD-TYPE
  T1             4             151
  T2             6             255
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PADI2 MUTATED     9   0     1
  PADI2 WILD-TYPE 298  89    71
D161V5, multiclass
       clus
vv      PADI2 MUTATED PADI2 WILD-TYPE
  N0                9             298
  N1                0              89
  N2+N3             1              71
[1] 3 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
  PADI2 MUTATED     7   1
  PADI2 WILD-TYPE 320  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI2 MUTATED      7    1
  PADI2 WILD-TYPE  320   22
   clus
vv  PADI2 MUTATED PADI2 WILD-TYPE
  0             7             320
  1             1              22
[1] 2 2
[1] FALSE
D161V7, binary
                 cls
clus                0   1
  PADI2 MUTATED     4   6
  PADI2 WILD-TYPE 255 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI2 MUTATED      4    6
  PADI2 WILD-TYPE  255  215
        clus
vv       PADI2 MUTATED PADI2 WILD-TYPE
  FEMALE             4             255
  MALE               6             215
[1] 2 2
[1] FALSE
D161V8, continuous
[1] "Remove cluster labels:" "PADI2 MUTATED"         
clus
  PADI2 MUTATED PADI2 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7711      TCGA-86-7713 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"PADI2 WILD-TYPE" "PADI2 WILD-TYPE" "PADI2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PADI2 MUTATED                            1                                 1
  PADI2 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PADI2 MUTATED                                                    7
  PADI2 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PADI2 MUTATED                                            0
  PADI2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PADI2 MUTATED                                               0
  PADI2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PADI2 MUTATED                                0
  PADI2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PADI2 MUTATED                                    0
  PADI2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PADI2 MUTATED                              0                             0
  PADI2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PADI2 MUTATED                                               1
  PADI2 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PADI2 MUTATED                              0
  PADI2 WILD-TYPE                            9
D161V9, multiclass
                                                    clus
vv                                                   PADI2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PADI2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V10, binary
                 cls
clus                0   1
  PADI2 MUTATED     1   9
  PADI2 WILD-TYPE  19 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI2 MUTATED      1    9
  PADI2 WILD-TYPE   19  451
     clus
vv    PADI2 MUTATED PADI2 WILD-TYPE
  NO              1              19
  YES             9             451
[1] 2 2
[1] FALSE
D161V11, continuous
D161V12, continuous
                 vv
clus               R0  R1  R2  RX
  PADI2 MUTATED     7   0   0   1
  PADI2 WILD-TYPE 303  11   4  24
D161V13, multiclass
    clus
vv   PADI2 MUTATED PADI2 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PADI2 MUTATED                                  0     0
  PADI2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PADI2 MUTATED                           1     8
  PADI2 WILD-TYPE                        28   369
D161V14, multiclass
                                  clus
vv                                 PADI2 MUTATED PADI2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V15, binary
                 cls
clus                0   1
  PADI2 MUTATED     0   8
  PADI2 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI2 MUTATED      0    8
  PADI2 WILD-TYPE    6  341
                        clus
vv                       PADI2 MUTATED PADI2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(162) Variable = C1ORF116 MUTATION ANALYSIS
D162V1, survival
                    sevent
clus2                  0   1
  C1ORF116 MUTATED     9   2
  C1ORF116 WILD-TYPE 306 139
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                11                445 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 2                139 
$`C1ORF116 MUTATED`
TCGA-44-2656 TCGA-49-4507 TCGA-55-8207 TCGA-55-8506 TCGA-55-A48Y TCGA-64-5775 
       46.98         8.81         2.17         0.36        20.71         2.04 
TCGA-69-7765 TCGA-73-7499 TCGA-78-7539 TCGA-86-8056 TCGA-91-6831 
        5.42        23.51        10.75         4.57        10.19 

$`C1ORF116 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       12.66        35.54        46.72        14.07        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        16.93        22.65        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       55.43        38.37        87.98        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       13.87         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1.25        39.09       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        53.33        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
       19.89        16.70        24.49         4.08        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36         1.97         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
              0.36               0.00 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
             46.98             223.96 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
              8.81              18.18 
[1] "0.4 - 47.0 (8.8)"   "0.0 - 224.0 (18.2)"
[1] "hr=" "1.2"
D162V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C1ORF116 MUTATED         0        0        4         2         1          3
  C1ORF116 WILD-TYPE       4      123      129        44        66         67
                    vv
clus                 STAGE IIIB STAGE IV
  C1ORF116 MUTATED            0        1
  C1ORF116 WILD-TYPE         11       24
D162V3, multiclass
            clus
vv           C1ORF116 MUTATED C1ORF116 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                123
  STAGE IB                  4                129
  STAGE IIA                 2                 44
  STAGE IIB                 1                 66
  STAGE IIIA                3                 67
  STAGE IIIB                0                 11
  STAGE IV                  1                 24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF116 MUTATED     0   6   2   3
  C1ORF116 WILD-TYPE 155 255  41  15
D162V4, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  T1                0                155
  T2                6                255
  T3                2                 41
  T4                3                 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"
                    vv
clus                  N0  N1 N2+N3
  C1ORF116 MUTATED    10   1     0
  C1ORF116 WILD-TYPE 297  88    72
D162V5, multiclass
       clus
vv      C1ORF116 MUTATED C1ORF116 WILD-TYPE
  N0                  10                297
  N1                   1                 88
  N2+N3                0                 72
[1] 3 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
  C1ORF116 MUTATED     7   0
  C1ORF116 WILD-TYPE 320  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      7    0
  C1ORF116 WILD-TYPE  320   23
   clus
vv  C1ORF116 MUTATED C1ORF116 WILD-TYPE
  0                7                320
  1                0                 23
[1] 2 2
[1] FALSE
D162V7, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     5   6
  C1ORF116 WILD-TYPE 254 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      5    6
  C1ORF116 WILD-TYPE  254  215
        clus
vv       C1ORF116 MUTATED C1ORF116 WILD-TYPE
  FEMALE                5                254
  MALE                  6                215
[1] 2 2
[1] FALSE
D162V8, continuous
[1] "Remove cluster labels:" "C1ORF116 MUTATED"      
clus
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 2                 82 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-7283         TCGA-55-7573 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-55-7725         TCGA-55-7910         TCGA-55-7914 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8096         TCGA-55-8205 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8507         TCGA-55-8508 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8619 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-55-8620         TCGA-55-A48Z         TCGA-55-A490 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-55-A494         TCGA-62-8394         TCGA-62-8395 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-62-8397         TCGA-62-8398         TCGA-62-8399 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-62-8402         TCGA-62-A46O         TCGA-62-A46P 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-62-A46R         TCGA-62-A46S         TCGA-62-A46U 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-62-A46V         TCGA-62-A46Y         TCGA-62-A470 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-62-A471         TCGA-62-A472         TCGA-64-1677 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-64-1681         TCGA-64-5778         TCGA-69-7974 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-69-8254         TCGA-71-6725         TCGA-71-8520 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-73-4659         TCGA-73-4662         TCGA-73-4666 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-73-4668         TCGA-73-4676         TCGA-73-7498 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-75-5122         TCGA-83-5908         TCGA-86-7701 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-86-7711         TCGA-86-7713         TCGA-86-7714 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-86-7954         TCGA-86-7955         TCGA-86-8055 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-86-8074         TCGA-86-8075         TCGA-86-8076 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-86-8278         TCGA-86-8279         TCGA-86-8281 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-86-8358         TCGA-86-8359         TCGA-86-8668 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-86-8669         TCGA-86-8671         TCGA-86-A4JF 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-86-A4P7         TCGA-91-6849         TCGA-93-7348 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-93-8067         TCGA-93-A4JN         TCGA-93-A4JO 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-99-7458         TCGA-MN-A4N1         TCGA-MN-A4N4 
"C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" "C1ORF116 WILD-TYPE" 
        TCGA-MN-A4N5 
"C1ORF116 WILD-TYPE" 
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  C1ORF116 MUTATED                            1
  C1ORF116 WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  C1ORF116 MUTATED                                   4
  C1ORF116 WILD-TYPE                                98
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C1ORF116 MUTATED                                                    6
  C1ORF116 WILD-TYPE                                                288
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C1ORF116 MUTATED                                            0
  C1ORF116 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C1ORF116 MUTATED                                               0
  C1ORF116 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  C1ORF116 MUTATED                                0
  C1ORF116 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  C1ORF116 MUTATED                                    0
  C1ORF116 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C1ORF116 MUTATED                              0                             0
  C1ORF116 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C1ORF116 MUTATED                                               0
  C1ORF116 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  C1ORF116 MUTATED                              0
  C1ORF116 WILD-TYPE                            9
D162V9, multiclass
                                                    clus
vv                                                   C1ORF116 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   C1ORF116 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V10, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     1  10
  C1ORF116 WILD-TYPE  19 450
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      1   10
  C1ORF116 WILD-TYPE   19  450
     clus
vv    C1ORF116 MUTATED C1ORF116 WILD-TYPE
  NO                 1                 19
  YES               10                450
[1] 2 2
[1] FALSE
D162V11, continuous
D162V12, continuous
                    vv
clus                  R0  R1  R2  RX
  C1ORF116 MUTATED     8   0   0   0
  C1ORF116 WILD-TYPE 302  11   4  25
D162V13, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  R0                8                302
  R1                0                 11
  R2                0                  4
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF116 MUTATED                                  0     0
  C1ORF116 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF116 MUTATED                           1    10
  C1ORF116 WILD-TYPE                        28   367
D162V14, multiclass
                                  clus
vv                                 C1ORF116 MUTATED C1ORF116 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       1                 28
  WHITE                                          10                367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V15, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     0  10
  C1ORF116 WILD-TYPE   6 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      0   10
  C1ORF116 WILD-TYPE    6  339
                        clus
vv                       C1ORF116 MUTATED C1ORF116 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               10                339
[1] 2 2
[1] FALSE

Clustering(163) Variable = NBPF3 MUTATION ANALYSIS
D163V1, survival
                 sevent
clus2               0   1
  NBPF3 MUTATED     4   2
  NBPF3 WILD-TYPE 311 139
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              6             450 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              2             139 
$`NBPF3 MUTATED`
TCGA-62-A46O TCGA-78-7162 TCGA-86-8054 TCGA-99-8025 TCGA-MP-A4TH TCGA-NJ-A4YF 
       47.80       104.19        24.49        34.85        14.66        71.05 

$`NBPF3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        7.07       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.43        19.89        16.70         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       11.05        14.10        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  NBPF3 MUTATED NBPF3 WILD-TYPE 
          14.66            0.00 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
         104.19          223.96 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
         41.325          17.835 
[1] "14.7 - 104.2 (41.3)" "0.0 - 224.0 (17.8)" 
[1] "hr=" "2.3"
D163V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NBPF3 MUTATED         0        3        1         0         1          1
  NBPF3 WILD-TYPE       4      120      132        46        66         69
                 vv
clus              STAGE IIIB STAGE IV
  NBPF3 MUTATED            0        0
  NBPF3 WILD-TYPE         11       25
D163V3, multiclass
            clus
vv           NBPF3 MUTATED NBPF3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               1             132
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NBPF3 MUTATED     3   2   1   0
  NBPF3 WILD-TYPE 152 259  42  18
D163V4, multiclass
    clus
vv   NBPF3 MUTATED NBPF3 WILD-TYPE
  T1             3             152
  T2             2             259
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  NBPF3 MUTATED     4   1     1
  NBPF3 WILD-TYPE 303  88    71
D163V5, multiclass
       clus
vv      NBPF3 MUTATED NBPF3 WILD-TYPE
  N0                4             303
  N1                1              88
  N2+N3             1              71
[1] 3 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
  NBPF3 MUTATED     6   0
  NBPF3 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      6    0
  NBPF3 WILD-TYPE  321   23
   clus
vv  NBPF3 MUTATED NBPF3 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D163V7, binary
                 cls
clus                0   1
  NBPF3 MUTATED     4   2
  NBPF3 WILD-TYPE 255 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      4    2
  NBPF3 WILD-TYPE  255  219
        clus
vv       NBPF3 MUTATED NBPF3 WILD-TYPE
  FEMALE             4             255
  MALE               2             219
[1] 2 2
[1] FALSE
D163V8, continuous
[1] "Remove cluster labels:" "NBPF3 MUTATED"         
clus
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" "NBPF3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NBPF3 MUTATED                            1                                 2
  NBPF3 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NBPF3 MUTATED                                                    3
  NBPF3 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NBPF3 MUTATED                                            0
  NBPF3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NBPF3 MUTATED                                               0
  NBPF3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NBPF3 MUTATED                                0
  NBPF3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NBPF3 MUTATED                                    0
  NBPF3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NBPF3 MUTATED                              0                             0
  NBPF3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NBPF3 MUTATED                                               0
  NBPF3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NBPF3 MUTATED                              0
  NBPF3 WILD-TYPE                            9
D163V9, multiclass
                                                    clus
vv                                                   NBPF3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NBPF3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V10, binary
                 cls
clus                0   1
  NBPF3 MUTATED     0   6
  NBPF3 WILD-TYPE  20 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      0    6
  NBPF3 WILD-TYPE   20  454
     clus
vv    NBPF3 MUTATED NBPF3 WILD-TYPE
  NO              0              20
  YES             6             454
[1] 2 2
[1] FALSE
D163V11, continuous
D163V12, continuous
                 vv
clus               R0  R1  R2  RX
  NBPF3 MUTATED     5   0   0   0
  NBPF3 WILD-TYPE 305  11   4  25
D163V13, multiclass
    clus
vv   NBPF3 MUTATED NBPF3 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBPF3 MUTATED                                  0     0
  NBPF3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NBPF3 MUTATED                           2     4
  NBPF3 WILD-TYPE                        27   373
D163V14, multiclass
                                  clus
vv                                 NBPF3 MUTATED NBPF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V15, binary
                 cls
clus                0   1
  NBPF3 MUTATED     0   5
  NBPF3 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      0    5
  NBPF3 WILD-TYPE    6  344
                        clus
vv                       NBPF3 MUTATED NBPF3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(164) Variable = RNMT MUTATION ANALYSIS
D164V1, survival
                sevent
clus2              0   1
  RNMT MUTATED     3   3
  RNMT WILD-TYPE 312 138
  RNMT MUTATED RNMT WILD-TYPE 
             6            450 
  RNMT MUTATED RNMT WILD-TYPE 
             3            138 
$`RNMT MUTATED`
TCGA-50-5933 TCGA-55-7995 TCGA-55-A491 TCGA-78-7145 TCGA-91-6829 TCGA-99-7458 
       78.67         0.16        20.58        27.16        41.36        24.56 

$`RNMT WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        14.27        40.60        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40         1.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       23.51       163.10         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 
       20.52        17.75        20.84        18.67        20.68        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  RNMT MUTATED RNMT WILD-TYPE 
          0.16           0.00 
  RNMT MUTATED RNMT WILD-TYPE 
         78.67         223.96 
  RNMT MUTATED RNMT WILD-TYPE 
        25.860         17.835 
[1] "0.2 - 78.7 (25.9)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D164V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RNMT MUTATED         0        2        2         0         0          1
  RNMT WILD-TYPE       4      121      131        46        67         69
                vv
clus             STAGE IIIB STAGE IV
  RNMT MUTATED            1        1
  RNMT WILD-TYPE         10       24
D164V3, multiclass
            clus
vv           RNMT MUTATED RNMT WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              2            131
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            1             69
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   2   0   3
  RNMT WILD-TYPE 153 259  43  15
D164V4, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  T1            2            153
  T2            2            259
  T3            0             43
  T4            3             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"
                vv
clus              N0  N1 N2+N3
  RNMT MUTATED     5   1     1
  RNMT WILD-TYPE 302  88    71
D164V5, multiclass
       clus
vv      RNMT MUTATED RNMT WILD-TYPE
  N0               5            302
  N1               1             88
  N2+N3            1             71
[1] 3 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
  RNMT MUTATED     4   1
  RNMT WILD-TYPE 323  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      4    1
  RNMT WILD-TYPE  323   22
   clus
vv  RNMT MUTATED RNMT WILD-TYPE
  0            4            323
  1            1             22
[1] 2 2
[1] FALSE
D164V7, binary
                cls
clus               0   1
  RNMT MUTATED     4   3
  RNMT WILD-TYPE 255 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      4    3
  RNMT WILD-TYPE  255  218
        clus
vv       RNMT MUTATED RNMT WILD-TYPE
  FEMALE            4            255
  MALE              3            218
[1] 2 2
[1] FALSE
D164V8, continuous
[1] "Remove cluster labels:" "RNMT MUTATED"          
clus
  RNMT MUTATED RNMT WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7711 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7954     TCGA-86-7955 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8074     TCGA-86-8075 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8281 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"RNMT WILD-TYPE" "RNMT WILD-TYPE" "RNMT WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RNMT MUTATED                            0                                 0
  RNMT WILD-TYPE                         18                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RNMT MUTATED                                                    5
  RNMT WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RNMT MUTATED                                            0
  RNMT WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RNMT MUTATED                                               2
  RNMT WILD-TYPE                                            17
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RNMT MUTATED                                0
  RNMT WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RNMT MUTATED                                    0
  RNMT WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RNMT MUTATED                              0                             0
  RNMT WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RNMT MUTATED                                               0
  RNMT WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RNMT MUTATED                              0
  RNMT WILD-TYPE                            9
D164V9, multiclass
                                                    clus
vv                                                   RNMT MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 2
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RNMT WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V10, binary
                cls
clus               0   1
  RNMT MUTATED     1   6
  RNMT WILD-TYPE  19 454
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      1    6
  RNMT WILD-TYPE   19  454
     clus
vv    RNMT MUTATED RNMT WILD-TYPE
  NO             1             19
  YES            6            454
[1] 2 2
[1] FALSE
D164V11, continuous
D164V12, continuous
                vv
clus              R0  R1  R2  RX
  RNMT MUTATED     5   1   0   0
  RNMT WILD-TYPE 305  10   4  25
D164V13, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  R0            5            305
  R1            1             10
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNMT MUTATED                                  0     0
  RNMT WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RNMT MUTATED                           0     6
  RNMT WILD-TYPE                        29   371
D164V14, multiclass
                                  clus
vv                                 RNMT MUTATED RNMT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       6            371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V15, binary
                cls
clus               0   1
  RNMT MUTATED     0   5
  RNMT WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      0    5
  RNMT WILD-TYPE    6  344
                        clus
vv                       RNMT MUTATED RNMT WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(165) Variable = PXK MUTATION ANALYSIS
D165V1, survival
               sevent
clus2             0   1
  PXK MUTATED     4   2
  PXK WILD-TYPE 311 139
  PXK MUTATED PXK WILD-TYPE 
            6           450 
  PXK MUTATED PXK WILD-TYPE 
            2           139 
$`PXK MUTATED`
TCGA-05-4427 TCGA-05-4432 TCGA-38-4625 TCGA-64-1679 TCGA-91-6829 TCGA-NJ-A4YI 
       26.01        25.02        97.74        55.43        41.36         0.13 

$`PXK WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       30.02        21.99        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        20.65        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  PXK MUTATED PXK WILD-TYPE 
         0.13          0.00 
  PXK MUTATED PXK WILD-TYPE 
        97.74        223.96 
  PXK MUTATED PXK WILD-TYPE 
       33.685        17.835 
[1] "0.1 - 97.7 (33.7)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.8"
D165V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PXK MUTATED         0        0        3         0         2          2
  PXK WILD-TYPE       4      123      130        46        65         68
               vv
clus            STAGE IIIB STAGE IV
  PXK MUTATED            0        0
  PXK WILD-TYPE         11       25
D165V3, multiclass
            clus
vv           PXK MUTATED PXK WILD-TYPE
  STAGE I              0             4
  STAGE IA             0           123
  STAGE IB             3           130
  STAGE IIA            0            46
  STAGE IIB            2            65
  STAGE IIIA           2            68
  STAGE IIIB           0            11
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PXK MUTATED     1   5   1   0
  PXK WILD-TYPE 154 256  42  18
D165V4, multiclass
    clus
vv   PXK MUTATED PXK WILD-TYPE
  T1           1           154
  T2           5           256
  T3           1            42
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  PXK MUTATED     3   2     2
  PXK WILD-TYPE 304  87    70
D165V5, multiclass
       clus
vv      PXK MUTATED PXK WILD-TYPE
  N0              3           304
  N1              2            87
  N2+N3           2            70
[1] 3 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
  PXK MUTATED     6   0
  PXK WILD-TYPE 321  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  PXK MUTATED      6    0
  PXK WILD-TYPE  321   23
   clus
vv  PXK MUTATED PXK WILD-TYPE
  0           6           321
  1           0            23
[1] 2 2
[1] FALSE
D165V7, binary
               cls
clus              0   1
  PXK MUTATED     4   3
  PXK WILD-TYPE 255 218
[1] "tbl2"
               cls
clus            [,1] [,2]
  PXK MUTATED      4    3
  PXK WILD-TYPE  255  218
        clus
vv       PXK MUTATED PXK WILD-TYPE
  FEMALE           4           255
  MALE             3           218
[1] 2 2
[1] FALSE
D165V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PXK MUTATED                            0                                 2
  PXK WILD-TYPE                         18                               100
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PXK MUTATED                                                    3
  PXK WILD-TYPE                                                291
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PXK MUTATED                                            0
  PXK WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PXK MUTATED                                               1
  PXK WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  PXK MUTATED                                0
  PXK WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  PXK MUTATED                                    0                            0
  PXK WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  PXK MUTATED                               1
  PXK WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PXK MUTATED                                               0
  PXK WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  PXK MUTATED                              0
  PXK WILD-TYPE                            9
D165V9, multiclass
                                                    clus
vv                                                   PXK MUTATED PXK WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            2           100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           3           291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V10, binary
               cls
clus              0   1
  PXK MUTATED     0   7
  PXK WILD-TYPE  20 453
[1] "tbl2"
               cls
clus            [,1] [,2]
  PXK MUTATED      0    7
  PXK WILD-TYPE   20  453
     clus
vv    PXK MUTATED PXK WILD-TYPE
  NO            0            20
  YES           7           453
[1] 2 2
[1] FALSE
D165V11, continuous
D165V12, continuous
               vv
clus             R0  R1  R2  RX
  PXK MUTATED     6   0   0   0
  PXK WILD-TYPE 304  11   4  25
D165V13, multiclass
    clus
vv   PXK MUTATED PXK WILD-TYPE
  R0           6           304
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PXK MUTATED                                  0     0
  PXK WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PXK MUTATED                           0     5
  PXK WILD-TYPE                        29   372
D165V14, multiclass
                                  clus
vv                                 PXK MUTATED PXK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                      5           372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V15, binary
               cls
clus              0   1
  PXK MUTATED     0   4
  PXK WILD-TYPE   6 345
[1] "tbl2"
               cls
clus            [,1] [,2]
  PXK MUTATED      0    4
  PXK WILD-TYPE    6  345
                        clus
vv                       PXK MUTATED PXK WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           4           345
[1] 2 2
[1] FALSE

Clustering(166) Variable = ZNF223 MUTATION ANALYSIS
D166V1, survival
                  sevent
clus2                0   1
  ZNF223 MUTATED     6   3
  ZNF223 WILD-TYPE 309 138
  ZNF223 MUTATED ZNF223 WILD-TYPE 
               9              447 
  ZNF223 MUTATED ZNF223 WILD-TYPE 
               3              138 
$`ZNF223 MUTATED`
TCGA-05-4390 TCGA-05-5420 TCGA-50-5930 TCGA-50-5946 TCGA-55-A493 TCGA-78-7539 
       37.02        15.02         9.27        22.55         0.92        10.75 
TCGA-86-6851 TCGA-86-7711 TCGA-91-6829 
        5.88        34.39        41.36 

$`ZNF223 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         8.22        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        20.58        19.59        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 
      110.50        27.09        12.36        31.13        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ZNF223 MUTATED ZNF223 WILD-TYPE 
            0.92             0.00 
  ZNF223 MUTATED ZNF223 WILD-TYPE 
           41.36           223.96 
  ZNF223 MUTATED ZNF223 WILD-TYPE 
           15.02            18.08 
[1] "0.9 - 41.4 (15.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D166V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF223 MUTATED         0        1        4         3         0          2
  ZNF223 WILD-TYPE       4      122      129        43        67         68
                  vv
clus               STAGE IIIB STAGE IV
  ZNF223 MUTATED            0        0
  ZNF223 WILD-TYPE         11       25
D166V3, multiclass
            clus
vv           ZNF223 MUTATED ZNF223 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                4              129
  STAGE IIA               3               43
  STAGE IIB               0               67
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF223 MUTATED     2   8   0   0
  ZNF223 WILD-TYPE 153 253  43  18
D166V4, multiclass
    clus
vv   ZNF223 MUTATED ZNF223 WILD-TYPE
  T1              2              153
  T2              8              253
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ZNF223 MUTATED     6   2     2
  ZNF223 WILD-TYPE 301  87    70
D166V5, multiclass
       clus
vv      ZNF223 MUTATED ZNF223 WILD-TYPE
  N0                 6              301
  N1                 2               87
  N2+N3              2               70
[1] 3 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
  ZNF223 MUTATED     8   0
  ZNF223 WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF223 MUTATED      8    0
  ZNF223 WILD-TYPE  319   23
   clus
vv  ZNF223 MUTATED ZNF223 WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D166V7, binary
                  cls
clus                 0   1
  ZNF223 MUTATED     4   6
  ZNF223 WILD-TYPE 255 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF223 MUTATED      4    6
  ZNF223 WILD-TYPE  255  215
        clus
vv       ZNF223 MUTATED ZNF223 WILD-TYPE
  FEMALE              4              255
  MALE                6              215
[1] 2 2
[1] FALSE
D166V8, continuous
[1] "Remove cluster labels:" "ZNF223 MUTATED"        
clus
  ZNF223 MUTATED ZNF223 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7713 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" "ZNF223 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF223 MUTATED                            0                                 5
  ZNF223 WILD-TYPE                         18                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF223 MUTATED                                                    4
  ZNF223 WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF223 MUTATED                                            0
  ZNF223 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF223 MUTATED                                               1
  ZNF223 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF223 MUTATED                                0
  ZNF223 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF223 MUTATED                                    0
  ZNF223 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF223 MUTATED                              0                             0
  ZNF223 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF223 MUTATED                                               0
  ZNF223 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF223 MUTATED                              0
  ZNF223 WILD-TYPE                            9
D166V9, multiclass
                                                    clus
vv                                                   ZNF223 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF223 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V10, binary
                  cls
clus                 0   1
  ZNF223 MUTATED     1   9
  ZNF223 WILD-TYPE  19 451
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF223 MUTATED      1    9
  ZNF223 WILD-TYPE   19  451
     clus
vv    ZNF223 MUTATED ZNF223 WILD-TYPE
  NO               1               19
  YES              9              451
[1] 2 2
[1] FALSE
D166V11, continuous
D166V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF223 MUTATED     7   0   0   0
  ZNF223 WILD-TYPE 303  11   4  25
D166V13, multiclass
    clus
vv   ZNF223 MUTATED ZNF223 WILD-TYPE
  R0              7              303
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF223 MUTATED                                  0     0
  ZNF223 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF223 MUTATED                           0     7
  ZNF223 WILD-TYPE                        29   370
D166V14, multiclass
                                  clus
vv                                 ZNF223 MUTATED ZNF223 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V15, binary
                  cls
clus                 0   1
  ZNF223 MUTATED     1   4
  ZNF223 WILD-TYPE   5 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF223 MUTATED      1    4
  ZNF223 WILD-TYPE    5  345
                        clus
vv                       ZNF223 MUTATED ZNF223 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(167) Variable = ASXL2 MUTATION ANALYSIS
D167V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED    16   2
  ASXL2 WILD-TYPE 299 139
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             438 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              2             139 
$`ASXL2 MUTATED`
TCGA-05-4396 TCGA-05-4430 TCGA-44-3398 TCGA-44-8119 TCGA-55-6972 TCGA-55-6984 
        9.96        25.02        38.24         3.25        48.49        24.99 
TCGA-55-7574 TCGA-55-8302 TCGA-55-8620 TCGA-55-A493 TCGA-64-5781 TCGA-71-8520 
        3.12         0.76         2.17         0.92        51.25         0.10 
TCGA-78-8640 TCGA-86-8054 TCGA-86-A4JF TCGA-91-6831 TCGA-95-7947 TCGA-NJ-A4YP 
      214.62        24.49        17.62        10.19        15.68         1.64 

$`ASXL2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       29.00        17.59        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        2.20        45.34        32.71        60.03        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
       14.01        13.45         4.24         7.04         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       10.55        32.68        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        16.70         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
       27.58         0.62        14.96        13.32        13.32        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 
        1.22         2.86        18.67        12.39        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13        29.13         0.26         0.43        19.82        59.11 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
            0.1             0.0 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         214.62          223.96 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         12.935          18.150 
[1] "0.1 - 214.6 (12.9)" "0.0 - 224.0 (18.1)"
[1] "hr=" "3.1"
D167V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ASXL2 MUTATED         0        2        9         1         4          0
  ASXL2 WILD-TYPE       4      121      124        45        63         70
                 vv
clus              STAGE IIIB STAGE IV
  ASXL2 MUTATED            1        1
  ASXL2 WILD-TYPE         10       24
D167V3, multiclass
            clus
vv           ASXL2 MUTATED ASXL2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               9             124
  STAGE IIA              1              45
  STAGE IIB              4              63
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASXL2 MUTATED     4  11   2   1
  ASXL2 WILD-TYPE 151 250  41  17
D167V4, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  T1             4             151
  T2            11             250
  T3             2              41
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  ASXL2 MUTATED    13   5     0
  ASXL2 WILD-TYPE 294  84    72
D167V5, multiclass
       clus
vv      ASXL2 MUTATED ASXL2 WILD-TYPE
  N0               13             294
  N1                5              84
  N2+N3             0              72
[1] 3 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
  ASXL2 MUTATED    15   1
  ASXL2 WILD-TYPE 312  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     15    1
  ASXL2 WILD-TYPE  312   22
   clus
vv  ASXL2 MUTATED ASXL2 WILD-TYPE
  0            15             312
  1             1              22
[1] 2 2
[1] FALSE
D167V7, binary
                 cls
clus                0   1
  ASXL2 MUTATED     7  11
  ASXL2 WILD-TYPE 252 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      7   11
  ASXL2 WILD-TYPE  252  210
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  FEMALE             7             252
  MALE              11             210
[1] 2 2
[1] FALSE
D167V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ASXL2 MUTATED                            1                                 4
  ASXL2 WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASXL2 MUTATED                                                   11
  ASXL2 WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ASXL2 MUTATED                                            0
  ASXL2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ASXL2 MUTATED                                               0
  ASXL2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ASXL2 MUTATED                                0
  ASXL2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ASXL2 MUTATED                                    0
  ASXL2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ASXL2 MUTATED                              0                             2
  ASXL2 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ASXL2 MUTATED                                               0
  ASXL2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ASXL2 MUTATED                              0
  ASXL2 WILD-TYPE                            9
D167V9, multiclass
                                                    clus
vv                                                   ASXL2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ASXL2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V10, binary
                 cls
clus                0   1
  ASXL2 MUTATED     1  17
  ASXL2 WILD-TYPE  19 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      1   17
  ASXL2 WILD-TYPE   19  443
     clus
vv    ASXL2 MUTATED ASXL2 WILD-TYPE
  NO              1              19
  YES            17             443
[1] 2 2
[1] FALSE
D167V11, continuous
D167V12, continuous
                 vv
clus               R0  R1  R2  RX
  ASXL2 MUTATED    13   1   0   0
  ASXL2 WILD-TYPE 297  10   4  25
D167V13, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  R0            13             297
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL2 MUTATED                                  0     1
  ASXL2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL2 MUTATED                           0    14
  ASXL2 WILD-TYPE                        29   363
D167V14, multiclass
                                  clus
vv                                 ASXL2 MUTATED ASXL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V15, binary
                 cls
clus                0   1
  ASXL2 MUTATED     0  14
  ASXL2 WILD-TYPE   6 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      0   14
  ASXL2 WILD-TYPE    6  335
                        clus
vv                       ASXL2 MUTATED ASXL2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            14             335
[1] 2 2
[1] FALSE

Clustering(168) Variable = CPA4 MUTATION ANALYSIS
D168V1, survival
                sevent
clus2              0   1
  CPA4 MUTATED    11   3
  CPA4 WILD-TYPE 304 138
  CPA4 MUTATED CPA4 WILD-TYPE 
            14            442 
  CPA4 MUTATED CPA4 WILD-TYPE 
             3            138 
$`CPA4 MUTATED`
TCGA-44-3396 TCGA-44-5644 TCGA-44-6147 TCGA-55-7907 TCGA-55-8089 TCGA-55-8302 
       37.15        28.37        27.78         0.53         3.29         0.76 
TCGA-55-A490 TCGA-78-7535 TCGA-86-7955 TCGA-97-8547 TCGA-97-A4M7 TCGA-99-8028 
        1.58        31.20        16.70        21.60        20.68        36.76 
TCGA-MP-A4TE TCGA-MP-A4TI 
       29.46        14.10 

$`CPA4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
       33.30        12.59        23.77        10.78         9.93        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.43        19.89        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        14.30        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       19.76        20.52        17.75        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
       31.23         2.43        10.09        11.05        14.66        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  CPA4 MUTATED CPA4 WILD-TYPE 
          0.53           0.00 
  CPA4 MUTATED CPA4 WILD-TYPE 
         37.15         223.96 
  CPA4 MUTATED CPA4 WILD-TYPE 
         21.14          17.95 
[1] "0.5 - 37.1 (21.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D168V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CPA4 MUTATED         0        4        4         4         0          2
  CPA4 WILD-TYPE       4      119      129        42        67         68
                vv
clus             STAGE IIIB STAGE IV
  CPA4 MUTATED            0        0
  CPA4 WILD-TYPE         11       25
D168V3, multiclass
            clus
vv           CPA4 MUTATED CPA4 WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              4            129
  STAGE IIA             4             42
  STAGE IIB             0             67
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPA4 MUTATED     4  10   0   0
  CPA4 WILD-TYPE 151 251  43  18
D168V4, multiclass
    clus
vv   CPA4 MUTATED CPA4 WILD-TYPE
  T1            4            151
  T2           10            251
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  CPA4 MUTATED     9   2     2
  CPA4 WILD-TYPE 298  87    70
D168V5, multiclass
       clus
vv      CPA4 MUTATED CPA4 WILD-TYPE
  N0               9            298
  N1               2             87
  N2+N3            2             70
[1] 3 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
  CPA4 MUTATED     8   0
  CPA4 WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPA4 MUTATED      8    0
  CPA4 WILD-TYPE  319   23
   clus
vv  CPA4 MUTATED CPA4 WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D168V7, binary
                cls
clus               0   1
  CPA4 MUTATED     5   9
  CPA4 WILD-TYPE 254 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPA4 MUTATED      5    9
  CPA4 WILD-TYPE  254  212
        clus
vv       CPA4 MUTATED CPA4 WILD-TYPE
  FEMALE            5            254
  MALE              9            212
[1] 2 2
[1] FALSE
D168V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CPA4 MUTATED                            0                                 2
  CPA4 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CPA4 MUTATED                                                   12
  CPA4 WILD-TYPE                                                282
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CPA4 MUTATED                                            0
  CPA4 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CPA4 MUTATED                                               0
  CPA4 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  CPA4 MUTATED                                0
  CPA4 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  CPA4 MUTATED                                    0
  CPA4 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CPA4 MUTATED                              0                             0
  CPA4 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CPA4 MUTATED                                               0
  CPA4 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  CPA4 MUTATED                              0
  CPA4 WILD-TYPE                            9
D168V9, multiclass
                                                    clus
vv                                                   CPA4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   CPA4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V10, binary
                cls
clus               0   1
  CPA4 MUTATED     0  14
  CPA4 WILD-TYPE  20 446
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPA4 MUTATED      0   14
  CPA4 WILD-TYPE   20  446
     clus
vv    CPA4 MUTATED CPA4 WILD-TYPE
  NO             0             20
  YES           14            446
[1] 2 2
[1] FALSE
D168V11, continuous
D168V12, continuous
                vv
clus              R0  R1  R2  RX
  CPA4 MUTATED     9   0   0   2
  CPA4 WILD-TYPE 301  11   4  23
D168V13, multiclass
    clus
vv   CPA4 MUTATED CPA4 WILD-TYPE
  R0            9            301
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPA4 MUTATED                                  0     0
  CPA4 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CPA4 MUTATED                           1    12
  CPA4 WILD-TYPE                        28   365
D168V14, multiclass
                                  clus
vv                                 CPA4 MUTATED CPA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      12            365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V15, binary
                cls
clus               0   1
  CPA4 MUTATED     0  11
  CPA4 WILD-TYPE   6 338
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPA4 MUTATED      0   11
  CPA4 WILD-TYPE    6  338
                        clus
vv                       CPA4 MUTATED CPA4 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           11            338
[1] 2 2
[1] FALSE

Clustering(169) Variable = SNX9 MUTATION ANALYSIS
D169V1, survival
                sevent
clus2              0   1
  SNX9 MUTATED     4   2
  SNX9 WILD-TYPE 311 139
  SNX9 MUTATED SNX9 WILD-TYPE 
             6            450 
  SNX9 MUTATED SNX9 WILD-TYPE 
             2            139 
$`SNX9 MUTATED`
TCGA-44-7667 TCGA-55-7727 TCGA-69-8253 TCGA-73-4677 TCGA-86-8672 TCGA-95-7043 
       36.07         1.12        14.01         1.25         0.62         1.22 

$`SNX9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.28         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30         2.93        12.56        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         1.32         5.39        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       14.60         1.15        13.91        30.84        27.58        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.12         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SNX9 MUTATED SNX9 WILD-TYPE 
          0.62           0.00 
  SNX9 MUTATED SNX9 WILD-TYPE 
         36.07         223.96 
  SNX9 MUTATED SNX9 WILD-TYPE 
         1.235         18.150 
[1] "0.6 - 36.1 (1.2)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "3"  
D169V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SNX9 MUTATED         0        2        0         1         3          1
  SNX9 WILD-TYPE       4      121      133        45        64         69
                vv
clus             STAGE IIIB STAGE IV
  SNX9 MUTATED            0        0
  SNX9 WILD-TYPE         11       25
D169V3, multiclass
            clus
vv           SNX9 MUTATED SNX9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              0            133
  STAGE IIA             1             45
  STAGE IIB             3             64
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SNX9 MUTATED     3   2   2   0
  SNX9 WILD-TYPE 152 259  41  18
D169V4, multiclass
    clus
vv   SNX9 MUTATED SNX9 WILD-TYPE
  T1            3            152
  T2            2            259
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  SNX9 MUTATED     4   2     1
  SNX9 WILD-TYPE 303  87    71
D169V5, multiclass
       clus
vv      SNX9 MUTATED SNX9 WILD-TYPE
  N0               4            303
  N1               2             87
  N2+N3            1             71
[1] 3 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
  SNX9 MUTATED     3   0
  SNX9 WILD-TYPE 324  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX9 MUTATED      3    0
  SNX9 WILD-TYPE  324   23
   clus
vv  SNX9 MUTATED SNX9 WILD-TYPE
  0            3            324
  1            0             23
[1] 2 2
[1] FALSE
D169V7, binary
                cls
clus               0   1
  SNX9 MUTATED     4   3
  SNX9 WILD-TYPE 255 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX9 MUTATED      4    3
  SNX9 WILD-TYPE  255  218
        clus
vv       SNX9 MUTATED SNX9 WILD-TYPE
  FEMALE            4            255
  MALE              3            218
[1] 2 2
[1] FALSE
D169V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SNX9 MUTATED                            0                                 2
  SNX9 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SNX9 MUTATED                                                    5
  SNX9 WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SNX9 MUTATED                                            0
  SNX9 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SNX9 MUTATED                                               0
  SNX9 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SNX9 MUTATED                                0
  SNX9 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SNX9 MUTATED                                    0
  SNX9 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SNX9 MUTATED                              0                             0
  SNX9 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SNX9 MUTATED                                               0
  SNX9 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SNX9 MUTATED                              0
  SNX9 WILD-TYPE                            9
D169V9, multiclass
                                                    clus
vv                                                   SNX9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SNX9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V10, binary
                cls
clus               0   1
  SNX9 MUTATED     0   7
  SNX9 WILD-TYPE  20 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX9 MUTATED      0    7
  SNX9 WILD-TYPE   20  453
     clus
vv    SNX9 MUTATED SNX9 WILD-TYPE
  NO             0             20
  YES            7            453
[1] 2 2
[1] FALSE
D169V11, continuous
D169V12, continuous
                vv
clus              R0  R1  R2  RX
  SNX9 MUTATED     4   0   0   0
  SNX9 WILD-TYPE 306  11   4  25
D169V13, multiclass
    clus
vv   SNX9 MUTATED SNX9 WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNX9 MUTATED                                  0     0
  SNX9 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SNX9 MUTATED                           1     5
  SNX9 WILD-TYPE                        28   372
D169V14, multiclass
                                  clus
vv                                 SNX9 MUTATED SNX9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V15, binary
                cls
clus               0   1
  SNX9 MUTATED     0   6
  SNX9 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX9 MUTATED      0    6
  SNX9 WILD-TYPE    6  343
                        clus
vv                       SNX9 MUTATED SNX9 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(170) Variable = BAP1 MUTATION ANALYSIS
D170V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED     6   2
  BAP1 WILD-TYPE 309 139
  BAP1 MUTATED BAP1 WILD-TYPE 
             8            448 
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            139 
$`BAP1 MUTATED`
TCGA-49-4506 TCGA-49-4510 TCGA-55-8506 TCGA-73-4670 TCGA-95-7948 TCGA-97-A4LX 
       32.84        29.46         0.36         4.31        15.65        20.19 
TCGA-97-A4M0 TCGA-97-A4M6 
       21.44        18.67 

$`BAP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 
       28.57        12.66        35.54        46.72        14.07         8.81 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
        1.22         2.86        18.67        12.39        15.68        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       14.30        21.60        20.58        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.36           0.00 
  BAP1 MUTATED BAP1 WILD-TYPE 
         32.84         223.96 
  BAP1 MUTATED BAP1 WILD-TYPE 
         19.43          17.95 
[1] "0.4 - 32.8 (19.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D170V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BAP1 MUTATED         0        1        3         0         3          0
  BAP1 WILD-TYPE       4      122      130        46        64         70
                vv
clus             STAGE IIIB STAGE IV
  BAP1 MUTATED            0        1
  BAP1 WILD-TYPE         11       24
D170V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAP1 MUTATED     1   6   1   0
  BAP1 WILD-TYPE 154 255  42  18
D170V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            1            154
  T2            6            255
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  BAP1 MUTATED     6   2     0
  BAP1 WILD-TYPE 301  87    72
D170V5, multiclass
       clus
vv      BAP1 MUTATED BAP1 WILD-TYPE
  N0               6            301
  N1               2             87
  N2+N3            0             72
[1] 3 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
  BAP1 MUTATED     6   1
  BAP1 WILD-TYPE 321  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      6    1
  BAP1 WILD-TYPE  321   22
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            6            321
  1            1             22
[1] 2 2
[1] FALSE
D170V7, binary
                cls
clus               0   1
  BAP1 MUTATED     7   1
  BAP1 WILD-TYPE 252 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      7    1
  BAP1 WILD-TYPE  252  220
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            7            252
  MALE              1            220
[1] 2 2
[1] FALSE
D170V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BAP1 MUTATED                            0                                 4
  BAP1 WILD-TYPE                         18                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BAP1 MUTATED                                                    4
  BAP1 WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BAP1 MUTATED                                            0
  BAP1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BAP1 MUTATED                                               0
  BAP1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  BAP1 MUTATED                                0
  BAP1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  BAP1 MUTATED                                    0
  BAP1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BAP1 MUTATED                              0                             0
  BAP1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BAP1 MUTATED                                               0
  BAP1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  BAP1 MUTATED                              0
  BAP1 WILD-TYPE                            9
D170V9, multiclass
                                                    clus
vv                                                   BAP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   BAP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V10, binary
                cls
clus               0   1
  BAP1 MUTATED     0   8
  BAP1 WILD-TYPE  20 452
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    8
  BAP1 WILD-TYPE   20  452
     clus
vv    BAP1 MUTATED BAP1 WILD-TYPE
  NO             0             20
  YES            8            452
[1] 2 2
[1] FALSE
D170V11, continuous
D170V12, continuous
                vv
clus              R0  R1  R2  RX
  BAP1 MUTATED     4   1   0   0
  BAP1 WILD-TYPE 306  10   4  25
D170V13, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0            4            306
  R1            1             10
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     0
  BAP1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           1     7
  BAP1 WILD-TYPE                        28   370
D170V14, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V15, binary
                cls
clus               0   1
  BAP1 MUTATED     0   8
  BAP1 WILD-TYPE   6 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    8
  BAP1 WILD-TYPE    6  341
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(171) Variable = PCSK4 MUTATION ANALYSIS
D171V1, survival
                 sevent
clus2               0   1
  PCSK4 MUTATED     7   1
  PCSK4 WILD-TYPE 308 140
  PCSK4 MUTATED PCSK4 WILD-TYPE 
              8             448 
  PCSK4 MUTATED PCSK4 WILD-TYPE 
              1             140 
$`PCSK4 MUTATED`
TCGA-44-8117 TCGA-44-8119 TCGA-53-7626 TCGA-55-8506 TCGA-67-3771 TCGA-69-7979 
       12.66         3.25        30.54         0.36        20.05         2.93 
TCGA-97-A4M7 TCGA-MN-A4N5 
       20.68         2.76 

$`PCSK4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        34.29        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.30        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  PCSK4 MUTATED PCSK4 WILD-TYPE 
           0.36            0.00 
  PCSK4 MUTATED PCSK4 WILD-TYPE 
          30.54          223.96 
  PCSK4 MUTATED PCSK4 WILD-TYPE 
          7.955          18.100 
[1] "0.4 - 30.5 (8.0)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D171V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PCSK4 MUTATED         0        3        2         1         2          0
  PCSK4 WILD-TYPE       4      120      131        45        65         70
                 vv
clus              STAGE IIIB STAGE IV
  PCSK4 MUTATED            0        0
  PCSK4 WILD-TYPE         11       25
D171V3, multiclass
            clus
vv           PCSK4 MUTATED PCSK4 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               2             131
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCSK4 MUTATED     4   2   2   0
  PCSK4 WILD-TYPE 151 259  41  18
D171V4, multiclass
    clus
vv   PCSK4 MUTATED PCSK4 WILD-TYPE
  T1             4             151
  T2             2             259
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PCSK4 MUTATED     7   1     0
  PCSK4 WILD-TYPE 300  88    72
D171V5, multiclass
       clus
vv      PCSK4 MUTATED PCSK4 WILD-TYPE
  N0                7             300
  N1                1              88
  N2+N3             0              72
[1] 3 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
  PCSK4 MUTATED     6   0
  PCSK4 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK4 MUTATED      6    0
  PCSK4 WILD-TYPE  321   23
   clus
vv  PCSK4 MUTATED PCSK4 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D171V7, binary
                 cls
clus                0   1
  PCSK4 MUTATED     5   3
  PCSK4 WILD-TYPE 254 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK4 MUTATED      5    3
  PCSK4 WILD-TYPE  254  218
        clus
vv       PCSK4 MUTATED PCSK4 WILD-TYPE
  FEMALE             5             254
  MALE               3             218
[1] 2 2
[1] FALSE
D171V8, continuous
[1] "Remove cluster labels:" "PCSK4 MUTATED"         
clus
  PCSK4 MUTATED PCSK4 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
     TCGA-99-7458      TCGA-MN-A4N1      TCGA-MN-A4N4 
"PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" "PCSK4 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PCSK4 MUTATED                            1                                 1
  PCSK4 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PCSK4 MUTATED                                                    6
  PCSK4 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PCSK4 MUTATED                                            0
  PCSK4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PCSK4 MUTATED                                               0
  PCSK4 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PCSK4 MUTATED                                0
  PCSK4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PCSK4 MUTATED                                    0
  PCSK4 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PCSK4 MUTATED                              0                             0
  PCSK4 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PCSK4 MUTATED                                               0
  PCSK4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PCSK4 MUTATED                              0
  PCSK4 WILD-TYPE                            9
D171V9, multiclass
                                                    clus
vv                                                   PCSK4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PCSK4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V10, binary
                 cls
clus                0   1
  PCSK4 MUTATED     0   8
  PCSK4 WILD-TYPE  20 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK4 MUTATED      0    8
  PCSK4 WILD-TYPE   20  452
     clus
vv    PCSK4 MUTATED PCSK4 WILD-TYPE
  NO              0              20
  YES             8             452
[1] 2 2
[1] FALSE
D171V11, continuous
D171V12, continuous
                 vv
clus               R0  R1  R2  RX
  PCSK4 MUTATED     5   0   0   0
  PCSK4 WILD-TYPE 305  11   4  25
D171V13, multiclass
    clus
vv   PCSK4 MUTATED PCSK4 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCSK4 MUTATED                                  0     0
  PCSK4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCSK4 MUTATED                           1     7
  PCSK4 WILD-TYPE                        28   370
D171V14, multiclass
                                  clus
vv                                 PCSK4 MUTATED PCSK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V15, binary
                 cls
clus                0   1
  PCSK4 MUTATED     0   8
  PCSK4 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK4 MUTATED      0    8
  PCSK4 WILD-TYPE    6  341
                        clus
vv                       PCSK4 MUTATED PCSK4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(172) Variable = FOLH1 MUTATION ANALYSIS
D172V1, survival
                 sevent
clus2               0   1
  FOLH1 MUTATED    20   8
  FOLH1 WILD-TYPE 295 133
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             28             428 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
              8             133 
$`FOLH1 MUTATED`
TCGA-05-4397 TCGA-44-3396 TCGA-44-3918 TCGA-44-5644 TCGA-44-5645 TCGA-44-6774 
       24.03        37.15        34.06        28.37        12.59        21.63 
TCGA-49-6743 TCGA-50-5931 TCGA-55-6969 TCGA-55-6982 TCGA-55-6987 TCGA-55-7227 
       12.13        14.27        40.73        32.71        70.26         1.74 
TCGA-55-7283 TCGA-55-7995 TCGA-55-8089 TCGA-55-8511 TCGA-55-A492 TCGA-55-A4DF 
        1.15         0.16         3.29         0.30        19.59        20.19 
TCGA-73-4666 TCGA-78-7145 TCGA-78-7155 TCGA-78-8640 TCGA-78-8660 TCGA-86-6851 
       26.30        27.16        38.50       214.62        10.55         5.88 
TCGA-86-7955 TCGA-86-A4JF TCGA-J2-A4AD TCGA-J2-A4AG 
       16.70        17.62        18.08        16.44 

$`FOLH1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 
       42.77        38.24         6.25        26.56        33.30        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
       10.78         9.93        27.78        23.15        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
        8.81        29.46        29.75        55.89        14.63        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        42.51        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
        5.49         7.79         2.20        45.34        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       40.54       107.21         0.59         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
       17.65         6.15        19.82        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
        1.58        20.58         0.92        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        29.98        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
        1.25        39.09        23.51       163.10         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       77.59       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       13.87        20.55        19.43        19.89        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
        5.59        24.30        23.80        35.47        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  FOLH1 MUTATED FOLH1 WILD-TYPE 
           0.16            0.00 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
         214.62          223.96 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
         18.835          17.950 
[1] "0.2 - 214.6 (18.8)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D172V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FOLH1 MUTATED         0        9        6         2         4          5
  FOLH1 WILD-TYPE       4      114      127        44        63         65
                 vv
clus              STAGE IIIB STAGE IV
  FOLH1 MUTATED            0        2
  FOLH1 WILD-TYPE         11       23
D172V3, multiclass
            clus
vv           FOLH1 MUTATED FOLH1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               9             114
  STAGE IB               6             127
  STAGE IIA              2              44
  STAGE IIB              4              63
  STAGE IIIA             5              65
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOLH1 MUTATED    14  10   3   1
  FOLH1 WILD-TYPE 141 251  40  17
D172V4, multiclass
    clus
vv   FOLH1 MUTATED FOLH1 WILD-TYPE
  T1            14             141
  T2            10             251
  T3             3              40
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  FOLH1 MUTATED    16   7     4
  FOLH1 WILD-TYPE 291  82    68
D172V5, multiclass
       clus
vv      FOLH1 MUTATED FOLH1 WILD-TYPE
  N0               16             291
  N1                7              82
  N2+N3             4              68
[1] 3 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
  FOLH1 MUTATED    16   2
  FOLH1 WILD-TYPE 311  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED     16    2
  FOLH1 WILD-TYPE  311   21
   clus
vv  FOLH1 MUTATED FOLH1 WILD-TYPE
  0            16             311
  1             2              21
[1] 2 2
[1] FALSE
D172V7, binary
                 cls
clus                0   1
  FOLH1 MUTATED    17  11
  FOLH1 WILD-TYPE 242 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED     17   11
  FOLH1 WILD-TYPE  242  210
        clus
vv       FOLH1 MUTATED FOLH1 WILD-TYPE
  FEMALE            17             242
  MALE              11             210
[1] 2 2
[1] FALSE
D172V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FOLH1 MUTATED                            0                                 2
  FOLH1 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FOLH1 MUTATED                                                   24
  FOLH1 WILD-TYPE                                                270
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FOLH1 MUTATED                                            0
  FOLH1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FOLH1 MUTATED                                               1
  FOLH1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FOLH1 MUTATED                                1
  FOLH1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FOLH1 MUTATED                                    0
  FOLH1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FOLH1 MUTATED                              0                             0
  FOLH1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FOLH1 MUTATED                                               0
  FOLH1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FOLH1 MUTATED                              0
  FOLH1 WILD-TYPE                            9
D172V9, multiclass
                                                    clus
vv                                                   FOLH1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            24
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FOLH1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V10, binary
                 cls
clus                0   1
  FOLH1 MUTATED     2  26
  FOLH1 WILD-TYPE  18 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED      2   26
  FOLH1 WILD-TYPE   18  434
     clus
vv    FOLH1 MUTATED FOLH1 WILD-TYPE
  NO              2              18
  YES            26             434
[1] 2 2
[1] FALSE
D172V11, continuous
D172V12, continuous
                 vv
clus               R0  R1  R2  RX
  FOLH1 MUTATED    15   1   0   2
  FOLH1 WILD-TYPE 295  10   4  23
D172V13, multiclass
    clus
vv   FOLH1 MUTATED FOLH1 WILD-TYPE
  R0            15             295
  R1             1              10
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOLH1 MUTATED                                  0     0
  FOLH1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOLH1 MUTATED                           1    24
  FOLH1 WILD-TYPE                        28   353
D172V14, multiclass
                                  clus
vv                                 FOLH1 MUTATED FOLH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       24             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V15, binary
                 cls
clus                0   1
  FOLH1 MUTATED     0  20
  FOLH1 WILD-TYPE   6 329
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED      0   20
  FOLH1 WILD-TYPE    6  329
                        clus
vv                       FOLH1 MUTATED FOLH1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            20             329
[1] 2 2
[1] FALSE

Clustering(173) Variable = ERLIN2 MUTATION ANALYSIS
D173V1, survival
                  sevent
clus2                0   1
  ERLIN2 MUTATED     1   5
  ERLIN2 WILD-TYPE 314 136
  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
               6              450 
  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
               5              136 
$`ERLIN2 MUTATED`
TCGA-44-7667 TCGA-64-1677 TCGA-78-7155 TCGA-86-8672 TCGA-MP-A4TA TCGA-MP-A4TK 
       36.07        20.65        38.50         0.62        31.23        19.13 

$`ERLIN2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
            0.62             0.00 
  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
           38.50           223.96 
  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
          25.940           17.835 
[1] "0.6 - 38.5 (25.9)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "2.7"
D173V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ERLIN2 MUTATED         0        1        1         0         3          1
  ERLIN2 WILD-TYPE       4      122      132        46        64         69
                  vv
clus               STAGE IIIB STAGE IV
  ERLIN2 MUTATED            0        0
  ERLIN2 WILD-TYPE         11       25
D173V3, multiclass
            clus
vv           ERLIN2 MUTATED ERLIN2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                1              132
  STAGE IIA               0               46
  STAGE IIB               3               64
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ERLIN2 MUTATED     1   3   2   0
  ERLIN2 WILD-TYPE 154 258  41  18
D173V4, multiclass
    clus
vv   ERLIN2 MUTATED ERLIN2 WILD-TYPE
  T1              1              154
  T2              3              258
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ERLIN2 MUTATED     4   1     1
  ERLIN2 WILD-TYPE 303  88    71
D173V5, multiclass
       clus
vv      ERLIN2 MUTATED ERLIN2 WILD-TYPE
  N0                 4              303
  N1                 1               88
  N2+N3              1               71
[1] 3 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
  ERLIN2 MUTATED     4   0
  ERLIN2 WILD-TYPE 323  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERLIN2 MUTATED      4    0
  ERLIN2 WILD-TYPE  323   23
   clus
vv  ERLIN2 MUTATED ERLIN2 WILD-TYPE
  0              4              323
  1              0               23
[1] 2 2
[1] FALSE
D173V7, binary
                  cls
clus                 0   1
  ERLIN2 MUTATED     4   2
  ERLIN2 WILD-TYPE 255 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERLIN2 MUTATED      4    2
  ERLIN2 WILD-TYPE  255  219
        clus
vv       ERLIN2 MUTATED ERLIN2 WILD-TYPE
  FEMALE              4              255
  MALE                2              219
[1] 2 2
[1] FALSE
D173V8, continuous
[1] "Remove cluster labels:" "ERLIN2 MUTATED"        
clus
  ERLIN2 MUTATED ERLIN2 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1681       TCGA-64-5778 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" "ERLIN2 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ERLIN2 MUTATED                            0                                 0
  ERLIN2 WILD-TYPE                         18                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ERLIN2 MUTATED                                                    6
  ERLIN2 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ERLIN2 MUTATED                                            0
  ERLIN2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ERLIN2 MUTATED                                               0
  ERLIN2 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ERLIN2 MUTATED                                0
  ERLIN2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ERLIN2 MUTATED                                    0
  ERLIN2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ERLIN2 MUTATED                              0                             0
  ERLIN2 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ERLIN2 MUTATED                                               0
  ERLIN2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ERLIN2 MUTATED                              0
  ERLIN2 WILD-TYPE                            9
D173V9, multiclass
                                                    clus
vv                                                   ERLIN2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ERLIN2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V10, binary
                  cls
clus                 0   1
  ERLIN2 MUTATED     0   6
  ERLIN2 WILD-TYPE  20 454
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERLIN2 MUTATED      0    6
  ERLIN2 WILD-TYPE   20  454
     clus
vv    ERLIN2 MUTATED ERLIN2 WILD-TYPE
  NO               0               20
  YES              6              454
[1] 2 2
[1] FALSE
D173V11, continuous
D173V12, continuous
                  vv
clus                R0  R1  R2  RX
  ERLIN2 MUTATED     5   0   0   0
  ERLIN2 WILD-TYPE 305  11   4  25
D173V13, multiclass
    clus
vv   ERLIN2 MUTATED ERLIN2 WILD-TYPE
  R0              5              305
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERLIN2 MUTATED                                  0     0
  ERLIN2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ERLIN2 MUTATED                           0     5
  ERLIN2 WILD-TYPE                        29   372
D173V14, multiclass
                                  clus
vv                                 ERLIN2 MUTATED ERLIN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V15, binary
                  cls
clus                 0   1
  ERLIN2 MUTATED     0   4
  ERLIN2 WILD-TYPE   6 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERLIN2 MUTATED      0    4
  ERLIN2 WILD-TYPE    6  345
                        clus
vv                       ERLIN2 MUTATED ERLIN2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(174) Variable = SBSN MUTATION ANALYSIS
D174V1, survival
                sevent
clus2              0   1
  SBSN MUTATED    11   1
  SBSN WILD-TYPE 304 140
  SBSN MUTATED SBSN WILD-TYPE 
            12            444 
  SBSN MUTATED SBSN WILD-TYPE 
             1            140 
$`SBSN MUTATED`
TCGA-05-4398 TCGA-44-8119 TCGA-50-5049 TCGA-55-7815 TCGA-55-7995 TCGA-55-A4DF 
       47.05         3.25        70.55         1.78         0.16        20.19 
TCGA-83-5908 TCGA-86-8054 TCGA-86-8358 TCGA-95-8039 TCGA-97-A4M0 TCGA-99-8025 
       27.09        24.49        21.47        27.29        21.44        34.85 

$`SBSN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 
       23.18         1.28         1.28         1.12         0.79         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       20.58        19.59         0.92        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        16.70         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.65         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SBSN MUTATED SBSN WILD-TYPE 
          0.16           0.00 
  SBSN MUTATED SBSN WILD-TYPE 
         70.55         223.96 
  SBSN MUTATED SBSN WILD-TYPE 
        22.980         17.735 
[1] "0.2 - 70.5 (23.0)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "4.1"
D174V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SBSN MUTATED         0        5        3         0         2          1
  SBSN WILD-TYPE       4      118      130        46        65         69
                vv
clus             STAGE IIIB STAGE IV
  SBSN MUTATED            1        0
  SBSN WILD-TYPE         10       25
D174V3, multiclass
            clus
vv           SBSN MUTATED SBSN WILD-TYPE
  STAGE I               0              4
  STAGE IA              5            118
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             2             65
  STAGE IIIA            1             69
  STAGE IIIB            1             10
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SBSN MUTATED     4   5   2   1
  SBSN WILD-TYPE 151 256  41  17
D174V4, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  T1            4            151
  T2            5            256
  T3            2             41
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  SBSN MUTATED     9   1     2
  SBSN WILD-TYPE 298  88    70
D174V5, multiclass
       clus
vv      SBSN MUTATED SBSN WILD-TYPE
  N0               9            298
  N1               1             88
  N2+N3            2             70
[1] 3 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
  SBSN MUTATED     9   0
  SBSN WILD-TYPE 318  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      9    0
  SBSN WILD-TYPE  318   23
   clus
vv  SBSN MUTATED SBSN WILD-TYPE
  0            9            318
  1            0             23
[1] 2 2
[1] FALSE
D174V7, binary
                cls
clus               0   1
  SBSN MUTATED     5   7
  SBSN WILD-TYPE 254 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      5    7
  SBSN WILD-TYPE  254  214
        clus
vv       SBSN MUTATED SBSN WILD-TYPE
  FEMALE            5            254
  MALE              7            214
[1] 2 2
[1] FALSE
D174V8, continuous
[1] "Remove cluster labels:" "SBSN MUTATED"          
clus
  SBSN MUTATED SBSN WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-75-5122     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8359 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SBSN MUTATED                            2                                 2
  SBSN WILD-TYPE                         16                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SBSN MUTATED                                                    8
  SBSN WILD-TYPE                                                286
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SBSN MUTATED                                            0
  SBSN WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SBSN MUTATED                                               0
  SBSN WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SBSN MUTATED                                0
  SBSN WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SBSN MUTATED                                    0
  SBSN WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SBSN MUTATED                              0                             0
  SBSN WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SBSN MUTATED                                               0
  SBSN WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SBSN MUTATED                              0
  SBSN WILD-TYPE                            9
D174V9, multiclass
                                                    clus
vv                                                   SBSN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SBSN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V10, binary
                cls
clus               0   1
  SBSN MUTATED     1  11
  SBSN WILD-TYPE  19 449
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      1   11
  SBSN WILD-TYPE   19  449
     clus
vv    SBSN MUTATED SBSN WILD-TYPE
  NO             1             19
  YES           11            449
[1] 2 2
[1] FALSE
D174V11, continuous
D174V12, continuous
                vv
clus              R0  R1  R2  RX
  SBSN MUTATED     8   0   0   1
  SBSN WILD-TYPE 302  11   4  24
D174V13, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  R0            8            302
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBSN MUTATED                                  0     0
  SBSN WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SBSN MUTATED                           1     9
  SBSN WILD-TYPE                        28   368
D174V14, multiclass
                                  clus
vv                                 SBSN MUTATED SBSN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       9            368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V15, binary
                cls
clus               0   1
  SBSN MUTATED     0  10
  SBSN WILD-TYPE   6 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      0   10
  SBSN WILD-TYPE    6  339
                        clus
vv                       SBSN MUTATED SBSN WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(175) Variable = NID2 MUTATION ANALYSIS
D175V1, survival
                sevent
clus2              0   1
  NID2 MUTATED    23  10
  NID2 WILD-TYPE 292 131
  NID2 MUTATED NID2 WILD-TYPE 
            33            423 
  NID2 MUTATED NID2 WILD-TYPE 
            10            131 
$`NID2 MUTATED`
TCGA-05-4420 TCGA-05-4427 TCGA-38-4626 TCGA-38-4629 TCGA-44-6779 TCGA-44-7662 
       29.98        26.01       120.79        28.41        16.44         7.17 
TCGA-50-5933 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6983 TCGA-55-7907 TCGA-55-7994 
       78.67        30.54         9.21        60.03         0.53        19.82 
TCGA-55-8092 TCGA-55-8302 TCGA-55-8616 TCGA-55-A4DF TCGA-69-7765 TCGA-69-7974 
        5.06         0.76         1.58        20.19         5.42         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K TCGA-73-4677 TCGA-78-8662 TCGA-86-6851 
        2.93        12.56         7.04         1.25       110.50         5.88 
TCGA-86-8073 TCGA-86-8358 TCGA-86-8674 TCGA-95-7562 TCGA-97-7554 TCGA-99-7458 
       24.33        21.47        13.32         2.86        25.48        24.56 
TCGA-J2-A4AG TCGA-MN-A4N1 TCGA-MP-A4TA 
       16.44        27.19        31.23 

$`NID2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68        97.74        37.71        49.05 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        32.45        61.28        14.60        19.46 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       12.03        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        14.27        40.60        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        25.61         7.59        27.25        34.29        13.94 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 
        5.49         7.79         2.20        45.34        32.71        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
       18.64         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.66        19.73         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
       13.61         7.56         2.30        14.01        13.45         4.24 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         1.32         5.39        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       77.59        10.55        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
       27.58         0.62        14.96        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         1.22        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 
       20.52        17.75        20.84        18.67        20.68        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 
       35.47        19.00        14.30         3.81         0.20        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  NID2 MUTATED NID2 WILD-TYPE 
          0.53           0.00 
  NID2 MUTATED NID2 WILD-TYPE 
        120.79         223.96 
  NID2 MUTATED NID2 WILD-TYPE 
         16.44          18.08 
[1] "0.5 - 120.8 (16.4)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D175V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NID2 MUTATED         1        4        8         8         7          3
  NID2 WILD-TYPE       3      119      125        38        60         67
                vv
clus             STAGE IIIB STAGE IV
  NID2 MUTATED            1        1
  NID2 WILD-TYPE         10       24
D175V3, multiclass
            clus
vv           NID2 MUTATED NID2 WILD-TYPE
  STAGE I               1              3
  STAGE IA              4            119
  STAGE IB              8            125
  STAGE IIA             8             38
  STAGE IIB             7             60
  STAGE IIIA            3             67
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of 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     6  20   4   3
  NID2 WILD-TYPE 149 241  39  15
D175V4, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  T1            6            149
  T2           20            241
  T3            4             39
  T4            3             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"
                vv
clus              N0  N1 N2+N3
  NID2 MUTATED    20  10     3
  NID2 WILD-TYPE 287  79    69
D175V5, multiclass
       clus
vv      NID2 MUTATED NID2 WILD-TYPE
  N0              20            287
  N1              10             79
  N2+N3            3             69
[1] 3 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
  NID2 MUTATED    21   0
  NID2 WILD-TYPE 306  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     21    0
  NID2 WILD-TYPE  306   23
   clus
vv  NID2 MUTATED NID2 WILD-TYPE
  0           21            306
  1            0             23
[1] 2 2
[1] FALSE
D175V7, binary
                cls
clus               0   1
  NID2 MUTATED    15  18
  NID2 WILD-TYPE 244 203
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     15   18
  NID2 WILD-TYPE  244  203
        clus
vv       NID2 MUTATED NID2 WILD-TYPE
  FEMALE           15            244
  MALE             18            203
[1] 2 2
[1] FALSE
D175V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NID2 MUTATED                            2                                 6
  NID2 WILD-TYPE                         16                                96
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NID2 MUTATED                                                   20
  NID2 WILD-TYPE                                                274
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NID2 MUTATED                                            0
  NID2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NID2 MUTATED                                               2
  NID2 WILD-TYPE                                            17
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  NID2 MUTATED                                0
  NID2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  NID2 MUTATED                                    0
  NID2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NID2 MUTATED                              0                             2
  NID2 WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NID2 MUTATED                                               0
  NID2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  NID2 MUTATED                              1
  NID2 WILD-TYPE                            8
D175V9, multiclass
                                                    clus
vv                                                   NID2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           20
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 2
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   NID2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            274
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V10, binary
                cls
clus               0   1
  NID2 MUTATED     2  31
  NID2 WILD-TYPE  18 429
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED      2   31
  NID2 WILD-TYPE   18  429
     clus
vv    NID2 MUTATED NID2 WILD-TYPE
  NO             2             18
  YES           31            429
[1] 2 2
[1] FALSE
D175V11, continuous
D175V12, continuous
                vv
clus              R0  R1  R2  RX
  NID2 MUTATED    22   0   0   2
  NID2 WILD-TYPE 288  11   4  23
D175V13, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  R0           22            288
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NID2 MUTATED                                  0     0
  NID2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NID2 MUTATED                           4    26
  NID2 WILD-TYPE                        25   351
D175V14, multiclass
                                  clus
vv                                 NID2 MUTATED NID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   4             25
  WHITE                                      26            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V15, binary
                cls
clus               0   1
  NID2 MUTATED     1  27
  NID2 WILD-TYPE   5 322
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED      1   27
  NID2 WILD-TYPE    5  322
                        clus
vv                       NID2 MUTATED NID2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           27            322
[1] 2 2
[1] FALSE

Clustering(176) Variable = SAMD7 MUTATION ANALYSIS
D176V1, survival
                 sevent
clus2               0   1
  SAMD7 MUTATED     8   2
  SAMD7 WILD-TYPE 307 139
  SAMD7 MUTATED SAMD7 WILD-TYPE 
             10             446 
  SAMD7 MUTATED SAMD7 WILD-TYPE 
              2             139 
$`SAMD7 MUTATED`
TCGA-05-4390 TCGA-05-5425 TCGA-35-5375 TCGA-44-A47A TCGA-49-4505 TCGA-49-6743 
       37.02        29.00         8.68        15.32        14.07        12.13 
TCGA-69-7765 TCGA-78-8662 TCGA-86-A4JF TCGA-99-7458 
        5.42       110.50        17.62        24.56 

$`SAMD7 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       13.87         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       32.68       214.62        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
       27.58         0.62        14.96        13.32        13.32        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SAMD7 MUTATED SAMD7 WILD-TYPE 
           5.42            0.00 
  SAMD7 MUTATED SAMD7 WILD-TYPE 
         110.50          223.96 
  SAMD7 MUTATED SAMD7 WILD-TYPE 
          16.47           18.10 
[1] "5.4 - 110.5 (16.5)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.9"
D176V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SAMD7 MUTATED         0        0        4         0         3          3
  SAMD7 WILD-TYPE       4      123      129        46        64         67
                 vv
clus              STAGE IIIB STAGE IV
  SAMD7 MUTATED            0        1
  SAMD7 WILD-TYPE         11       24
D176V3, multiclass
            clus
vv           SAMD7 MUTATED SAMD7 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SAMD7 MUTATED     1   7   1   2
  SAMD7 WILD-TYPE 154 254  42  16
D176V4, multiclass
    clus
vv   SAMD7 MUTATED SAMD7 WILD-TYPE
  T1             1             154
  T2             7             254
  T3             1              42
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  SAMD7 MUTATED     7   2     2
  SAMD7 WILD-TYPE 300  87    70
D176V5, multiclass
       clus
vv      SAMD7 MUTATED SAMD7 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             2              70
[1] 3 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
  SAMD7 MUTATED     8   0
  SAMD7 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD7 MUTATED      8    0
  SAMD7 WILD-TYPE  319   23
   clus
vv  SAMD7 MUTATED SAMD7 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D176V7, binary
                 cls
clus                0   1
  SAMD7 MUTATED     7   4
  SAMD7 WILD-TYPE 252 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD7 MUTATED      7    4
  SAMD7 WILD-TYPE  252  217
        clus
vv       SAMD7 MUTATED SAMD7 WILD-TYPE
  FEMALE             7             252
  MALE               4             217
[1] 2 2
[1] FALSE
D176V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SAMD7 MUTATED                            0                                 3
  SAMD7 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SAMD7 MUTATED                                                    6
  SAMD7 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SAMD7 MUTATED                                            0
  SAMD7 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SAMD7 MUTATED                                               1
  SAMD7 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SAMD7 MUTATED                                1
  SAMD7 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SAMD7 MUTATED                                    0
  SAMD7 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SAMD7 MUTATED                              0                             0
  SAMD7 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SAMD7 MUTATED                                               0
  SAMD7 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SAMD7 MUTATED                              0
  SAMD7 WILD-TYPE                            9
D176V9, multiclass
                                                    clus
vv                                                   SAMD7 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SAMD7 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V10, binary
                 cls
clus                0   1
  SAMD7 MUTATED     0  11
  SAMD7 WILD-TYPE  20 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD7 MUTATED      0   11
  SAMD7 WILD-TYPE   20  449
     clus
vv    SAMD7 MUTATED SAMD7 WILD-TYPE
  NO              0              20
  YES            11             449
[1] 2 2
[1] FALSE
D176V11, continuous
D176V12, continuous
                 vv
clus               R0  R1  R2  RX
  SAMD7 MUTATED     9   0   0   0
  SAMD7 WILD-TYPE 301  11   4  25
D176V13, multiclass
    clus
vv   SAMD7 MUTATED SAMD7 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMD7 MUTATED                                  0     0
  SAMD7 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SAMD7 MUTATED                           1     6
  SAMD7 WILD-TYPE                        28   371
D176V14, multiclass
                                  clus
vv                                 SAMD7 MUTATED SAMD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V15, binary
                 cls
clus                0   1
  SAMD7 MUTATED     0   6
  SAMD7 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD7 MUTATED      0    6
  SAMD7 WILD-TYPE    6  343
                        clus
vv                       SAMD7 MUTATED SAMD7 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(177) Variable = SERPINB5 MUTATION ANALYSIS
D177V1, survival
                    sevent
clus2                  0   1
  SERPINB5 MUTATED     7   1
  SERPINB5 WILD-TYPE 308 140
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 8                448 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 1                140 
$`SERPINB5 MUTATED`
TCGA-05-4405 TCGA-05-5423 TCGA-44-6774 TCGA-55-A494 TCGA-67-6215 TCGA-78-8662 
       20.05         4.96        21.63        15.81         5.72       110.50 
TCGA-86-7953 TCGA-86-8278 
       19.43        15.65 

$`SERPINB5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59         0.92        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       13.87        20.55        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        4.57        24.33         0.79        15.75        16.08        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
              4.96               0.00 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
            110.50             223.96 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
             17.62              18.03 
[1] "5.0 - 110.5 (17.6)" "0.0 - 224.0 (18.0)"
[1] "hr=" "3.1"
D177V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SERPINB5 MUTATED         0        1        4         0         2          2
  SERPINB5 WILD-TYPE       4      122      129        46        65         68
                    vv
clus                 STAGE IIIB STAGE IV
  SERPINB5 MUTATED            0        0
  SERPINB5 WILD-TYPE         11       25
D177V3, multiclass
            clus
vv           SERPINB5 MUTATED SERPINB5 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  1                122
  STAGE IB                  4                129
  STAGE IIA                 0                 46
  STAGE IIB                 2                 65
  STAGE IIIA                2                 68
  STAGE IIIB                0                 11
  STAGE IV                  0                 25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINB5 MUTATED     2   7   0   0
  SERPINB5 WILD-TYPE 153 254  43  18
D177V4, multiclass
    clus
vv   SERPINB5 MUTATED SERPINB5 WILD-TYPE
  T1                2                153
  T2                7                254
  T3                0                 43
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  SERPINB5 MUTATED     5   2     2
  SERPINB5 WILD-TYPE 302  87    70
D177V5, multiclass
       clus
vv      SERPINB5 MUTATED SERPINB5 WILD-TYPE
  N0                   5                302
  N1                   2                 87
  N2+N3                2                 70
[1] 3 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
  SERPINB5 MUTATED     8   0
  SERPINB5 WILD-TYPE 319  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      8    0
  SERPINB5 WILD-TYPE  319   23
   clus
vv  SERPINB5 MUTATED SERPINB5 WILD-TYPE
  0                8                319
  1                0                 23
[1] 2 2
[1] FALSE
D177V7, binary
                    cls
clus                   0   1
  SERPINB5 MUTATED     8   1
  SERPINB5 WILD-TYPE 251 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      8    1
  SERPINB5 WILD-TYPE  251  220
        clus
vv       SERPINB5 MUTATED SERPINB5 WILD-TYPE
  FEMALE                8                251
  MALE                  1                220
[1] 2 2
[1] FALSE
D177V8, continuous
[1] "Remove cluster labels:" "SERPINB5 MUTATED"      
clus
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 2                 82 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-7283         TCGA-55-7573 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-55-7725         TCGA-55-7910         TCGA-55-7914 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8096         TCGA-55-8205 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8507         TCGA-55-8508 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8619 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-55-8620         TCGA-55-A48Z         TCGA-55-A490 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-62-8394         TCGA-62-8395         TCGA-62-8397 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-62-8398         TCGA-62-8399         TCGA-62-8402 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-62-A46O         TCGA-62-A46P         TCGA-62-A46R 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-62-A46S         TCGA-62-A46U         TCGA-62-A46V 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-62-A46Y         TCGA-62-A470         TCGA-62-A471 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-62-A472         TCGA-64-1677         TCGA-64-1681 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-64-5778         TCGA-69-7974         TCGA-69-8254 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-71-6725         TCGA-71-8520         TCGA-73-4659 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-73-4662         TCGA-73-4666         TCGA-73-4668 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-73-4676         TCGA-73-7498         TCGA-73-7499 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-75-5122         TCGA-83-5908         TCGA-86-7701 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-86-7711         TCGA-86-7713         TCGA-86-7714 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-86-7954         TCGA-86-7955         TCGA-86-8055 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-86-8056         TCGA-86-8074         TCGA-86-8075 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-86-8076         TCGA-86-8279         TCGA-86-8281 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-86-8358         TCGA-86-8359         TCGA-86-8668 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-86-8669         TCGA-86-8671         TCGA-86-A4JF 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-86-A4P7         TCGA-91-6849         TCGA-93-7348 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-93-8067         TCGA-93-A4JN         TCGA-93-A4JO 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-99-7458         TCGA-MN-A4N1         TCGA-MN-A4N4 
"SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" "SERPINB5 WILD-TYPE" 
        TCGA-MN-A4N5 
"SERPINB5 WILD-TYPE" 
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  SERPINB5 MUTATED                            0
  SERPINB5 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  SERPINB5 MUTATED                                   2
  SERPINB5 WILD-TYPE                               100
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SERPINB5 MUTATED                                                    7
  SERPINB5 WILD-TYPE                                                287
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SERPINB5 MUTATED                                            0
  SERPINB5 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SERPINB5 MUTATED                                               0
  SERPINB5 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  SERPINB5 MUTATED                                0
  SERPINB5 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  SERPINB5 MUTATED                                    0
  SERPINB5 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SERPINB5 MUTATED                              0                             0
  SERPINB5 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SERPINB5 MUTATED                                               0
  SERPINB5 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  SERPINB5 MUTATED                              0
  SERPINB5 WILD-TYPE                            9
D177V9, multiclass
                                                    clus
vv                                                   SERPINB5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   SERPINB5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V10, binary
                    cls
clus                   0   1
  SERPINB5 MUTATED     1   8
  SERPINB5 WILD-TYPE  19 452
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      1    8
  SERPINB5 WILD-TYPE   19  452
     clus
vv    SERPINB5 MUTATED SERPINB5 WILD-TYPE
  NO                 1                 19
  YES                8                452
[1] 2 2
[1] FALSE
D177V11, continuous
D177V12, continuous
                    vv
clus                  R0  R1  R2  RX
  SERPINB5 MUTATED     7   0   0   1
  SERPINB5 WILD-TYPE 303  11   4  24
D177V13, multiclass
    clus
vv   SERPINB5 MUTATED SERPINB5 WILD-TYPE
  R0                7                303
  R1                0                 11
  R2                0                  4
  RX                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINB5 MUTATED                                  0     0
  SERPINB5 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SERPINB5 MUTATED                           0     5
  SERPINB5 WILD-TYPE                        29   372
D177V14, multiclass
                                  clus
vv                                 SERPINB5 MUTATED SERPINB5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       0                 29
  WHITE                                           5                372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V15, binary
                    cls
clus                   0   1
  SERPINB5 MUTATED     0   5
  SERPINB5 WILD-TYPE   6 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      0    5
  SERPINB5 WILD-TYPE    6  344
                        clus
vv                       SERPINB5 MUTATED SERPINB5 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                5                344
[1] 2 2
[1] FALSE

Clustering(178) Variable = SLC39A6 MUTATION ANALYSIS
D178V1, survival
                   sevent
clus2                 0   1
  SLC39A6 MUTATED     7   7
  SLC39A6 WILD-TYPE 308 134
  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
               14               442 
  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
                7               134 
$`SLC39A6 MUTATED`
TCGA-05-5425 TCGA-44-6778 TCGA-44-7671 TCGA-44-8120 TCGA-50-5045 TCGA-50-5072 
       29.00        61.28        17.59         8.55        71.47         8.22 
TCGA-50-5930 TCGA-50-6592 TCGA-55-1595 TCGA-55-6982 TCGA-64-1676 TCGA-MN-A4N5 
        9.27        25.55        48.62        32.71        56.81         2.76 
TCGA-MP-A4TA TCGA-NJ-A4YI 
       31.23         0.13 

$`SLC39A6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
       18.87        29.00        23.64        12.66         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
        5.49         7.79         2.20        45.34        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
       72.30        13.61        39.25        40.96        29.92        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19        38.63        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05        62.60         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
             0.13              0.00 
  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
            71.47            223.96 
  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
           27.275            17.950 
[1] "0.1 - 71.5 (27.3)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D178V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC39A6 MUTATED         0        6        3         0         2          3
  SLC39A6 WILD-TYPE       4      117      130        46        65         67
                   vv
clus                STAGE IIIB STAGE IV
  SLC39A6 MUTATED            0        0
  SLC39A6 WILD-TYPE         11       25
D178V3, multiclass
            clus
vv           SLC39A6 MUTATED SLC39A6 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 6               117
  STAGE IB                 3               130
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC39A6 MUTATED     5   9   0   0
  SLC39A6 WILD-TYPE 150 252  43  18
D178V4, multiclass
    clus
vv   SLC39A6 MUTATED SLC39A6 WILD-TYPE
  T1               5               150
  T2               9               252
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  SLC39A6 MUTATED     8   3     3
  SLC39A6 WILD-TYPE 299  86    69
D178V5, multiclass
       clus
vv      SLC39A6 MUTATED SLC39A6 WILD-TYPE
  N0                  8               299
  N1                  3                86
  N2+N3               3                69
[1] 3 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
  SLC39A6 MUTATED    13   0
  SLC39A6 WILD-TYPE 314  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A6 MUTATED     13    0
  SLC39A6 WILD-TYPE  314   23
   clus
vv  SLC39A6 MUTATED SLC39A6 WILD-TYPE
  0              13               314
  1               0                23
[1] 2 2
[1] FALSE
D178V7, binary
                   cls
clus                  0   1
  SLC39A6 MUTATED     6   8
  SLC39A6 WILD-TYPE 253 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A6 MUTATED      6    8
  SLC39A6 WILD-TYPE  253  213
        clus
vv       SLC39A6 MUTATED SLC39A6 WILD-TYPE
  FEMALE               6               253
  MALE                 8               213
[1] 2 2
[1] FALSE
D178V8, continuous
[1] "Remove cluster labels:" "SLC39A6 MUTATED"       
clus
  SLC39A6 MUTATED SLC39A6 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-93-7348        TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
       TCGA-99-7458        TCGA-MN-A4N1        TCGA-MN-A4N4 
"SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" "SLC39A6 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC39A6 MUTATED                            0
  SLC39A6 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC39A6 MUTATED                                   3
  SLC39A6 WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC39A6 MUTATED                                                    9
  SLC39A6 WILD-TYPE                                                285
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC39A6 MUTATED                                            0
  SLC39A6 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC39A6 MUTATED                                               0
  SLC39A6 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC39A6 MUTATED                                1
  SLC39A6 WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC39A6 MUTATED                                    0
  SLC39A6 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC39A6 MUTATED                              0                             1
  SLC39A6 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC39A6 MUTATED                                               0
  SLC39A6 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC39A6 MUTATED                              0
  SLC39A6 WILD-TYPE                            9
D178V9, multiclass
                                                    clus
vv                                                   SLC39A6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SLC39A6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V10, binary
                   cls
clus                  0   1
  SLC39A6 MUTATED     3  11
  SLC39A6 WILD-TYPE  17 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A6 MUTATED      3   11
  SLC39A6 WILD-TYPE   17  449
     clus
vv    SLC39A6 MUTATED SLC39A6 WILD-TYPE
  NO                3                17
  YES              11               449
[1] 2 2
[1] FALSE
D178V11, continuous
D178V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC39A6 MUTATED     4   0   0   0
  SLC39A6 WILD-TYPE 306  11   4  25
D178V13, multiclass
    clus
vv   SLC39A6 MUTATED SLC39A6 WILD-TYPE
  R0               4               306
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC39A6 MUTATED                                  0     1
  SLC39A6 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC39A6 MUTATED                           4     8
  SLC39A6 WILD-TYPE                        25   369
D178V14, multiclass
                                  clus
vv                                 SLC39A6 MUTATED SLC39A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      4                25
  WHITE                                          8               369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V15, binary
                   cls
clus                  0   1
  SLC39A6 MUTATED     0  10
  SLC39A6 WILD-TYPE   6 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A6 MUTATED      0   10
  SLC39A6 WILD-TYPE    6  339
                        clus
vv                       SLC39A6 MUTATED SLC39A6 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              10               339
[1] 2 2
[1] FALSE

Clustering(179) Variable = PHKA1 MUTATION ANALYSIS
D179V1, survival
                 sevent
clus2               0   1
  PHKA1 MUTATED    10   2
  PHKA1 WILD-TYPE 305 139
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             444 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
              2             139 
$`PHKA1 MUTATED`
TCGA-44-8117 TCGA-49-6767 TCGA-53-7626 TCGA-55-6970 TCGA-55-8506 TCGA-62-8399 
       12.66        22.26        30.54        15.25         0.36        88.64 
TCGA-64-1679 TCGA-67-3771 TCGA-78-7161 TCGA-86-7954 TCGA-86-8358 TCGA-L4-A4E5 
       55.43        20.05         7.07        19.89        21.47        19.00 

$`PHKA1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        34.29        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        40.73         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 
       39.25        40.96        29.92        56.81        20.65        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 
       38.50        32.09         5.88        64.90        22.29       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        35.47        16.44        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  PHKA1 MUTATED PHKA1 WILD-TYPE 
           0.36            0.00 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
          88.64          223.96 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
         19.970          17.835 
[1] "0.4 - 88.6 (20.0)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "2.2"
D179V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PHKA1 MUTATED         1        1        3         1         3          3
  PHKA1 WILD-TYPE       3      122      130        45        64         67
                 vv
clus              STAGE IIIB STAGE IV
  PHKA1 MUTATED            0        0
  PHKA1 WILD-TYPE         11       25
D179V3, multiclass
            clus
vv           PHKA1 MUTATED PHKA1 WILD-TYPE
  STAGE I                1               3
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              1              45
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PHKA1 MUTATED     4   5   3   0
  PHKA1 WILD-TYPE 151 256  40  18
D179V4, multiclass
    clus
vv   PHKA1 MUTATED PHKA1 WILD-TYPE
  T1             4             151
  T2             5             256
  T3             3              40
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PHKA1 MUTATED     8   1     3
  PHKA1 WILD-TYPE 299  88    69
D179V5, multiclass
       clus
vv      PHKA1 MUTATED PHKA1 WILD-TYPE
  N0                8             299
  N1                1              88
  N2+N3             3              69
[1] 3 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
  PHKA1 MUTATED     9   0
  PHKA1 WILD-TYPE 318  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      9    0
  PHKA1 WILD-TYPE  318   23
   clus
vv  PHKA1 MUTATED PHKA1 WILD-TYPE
  0             9             318
  1             0              23
[1] 2 2
[1] FALSE
D179V7, binary
                 cls
clus                0   1
  PHKA1 MUTATED    10   2
  PHKA1 WILD-TYPE 249 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED     10    2
  PHKA1 WILD-TYPE  249  219
        clus
vv       PHKA1 MUTATED PHKA1 WILD-TYPE
  FEMALE            10             249
  MALE               2             219
[1] 2 2
[1] FALSE
D179V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PHKA1 MUTATED                            0                                 1
  PHKA1 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PHKA1 MUTATED                                                    8
  PHKA1 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PHKA1 MUTATED                                            0
  PHKA1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PHKA1 MUTATED                                               1
  PHKA1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PHKA1 MUTATED                                0
  PHKA1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PHKA1 MUTATED                                    0
  PHKA1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PHKA1 MUTATED                              0                             2
  PHKA1 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PHKA1 MUTATED                                               0
  PHKA1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PHKA1 MUTATED                              0
  PHKA1 WILD-TYPE                            9
D179V9, multiclass
                                                    clus
vv                                                   PHKA1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PHKA1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V10, binary
                 cls
clus                0   1
  PHKA1 MUTATED     0  12
  PHKA1 WILD-TYPE  20 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      0   12
  PHKA1 WILD-TYPE   20  448
     clus
vv    PHKA1 MUTATED PHKA1 WILD-TYPE
  NO              0              20
  YES            12             448
[1] 2 2
[1] FALSE
D179V11, continuous
D179V12, continuous
                 vv
clus               R0  R1  R2  RX
  PHKA1 MUTATED     9   2   0   0
  PHKA1 WILD-TYPE 301   9   4  25
D179V13, multiclass
    clus
vv   PHKA1 MUTATED PHKA1 WILD-TYPE
  R0             9             301
  R1             2               9
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHKA1 MUTATED                                  0     0
  PHKA1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PHKA1 MUTATED                           1    11
  PHKA1 WILD-TYPE                        28   366
D179V14, multiclass
                                  clus
vv                                 PHKA1 MUTATED PHKA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V15, binary
                 cls
clus                0   1
  PHKA1 MUTATED     0   9
  PHKA1 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      0    9
  PHKA1 WILD-TYPE    6  340
                        clus
vv                       PHKA1 MUTATED PHKA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(180) Variable = KRT26 MUTATION ANALYSIS
D180V1, survival
                 sevent
clus2               0   1
  KRT26 MUTATED     7   2
  KRT26 WILD-TYPE 308 139
  KRT26 MUTATED KRT26 WILD-TYPE 
              9             447 
  KRT26 MUTATED KRT26 WILD-TYPE 
              2             139 
$`KRT26 MUTATED`
TCGA-38-4625 TCGA-44-8120 TCGA-49-4514 TCGA-55-8089 TCGA-78-8662 TCGA-86-8279 
       97.74         8.55        55.89         3.29       110.50        15.85 
TCGA-86-8669 TCGA-91-6829 TCGA-99-8028 
       30.84        41.36        36.76 

$`KRT26 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       16.08        15.65        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       17.62        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 
       18.67        20.68        24.56        34.85         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  KRT26 MUTATED KRT26 WILD-TYPE 
           3.29            0.00 
  KRT26 MUTATED KRT26 WILD-TYPE 
         110.50          223.96 
  KRT26 MUTATED KRT26 WILD-TYPE 
          36.76           17.92 
[1] "3.3 - 110.5 (36.8)" "0.0 - 224.0 (17.9)"
[1] "hr=" "3.2"
D180V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KRT26 MUTATED         0        4        4         1         0          0
  KRT26 WILD-TYPE       4      119      129        45        67         70
                 vv
clus              STAGE IIIB STAGE IV
  KRT26 MUTATED            0        0
  KRT26 WILD-TYPE         11       25
D180V3, multiclass
            clus
vv           KRT26 MUTATED KRT26 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT26 MUTATED     4   5   0   0
  KRT26 WILD-TYPE 151 256  43  18
D180V4, multiclass
    clus
vv   KRT26 MUTATED KRT26 WILD-TYPE
  T1             4             151
  T2             5             256
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  KRT26 MUTATED     8   1     0
  KRT26 WILD-TYPE 299  88    72
D180V5, multiclass
       clus
vv      KRT26 MUTATED KRT26 WILD-TYPE
  N0                8             299
  N1                1              88
  N2+N3             0              72
[1] 3 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
  KRT26 MUTATED     8   0
  KRT26 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT26 MUTATED      8    0
  KRT26 WILD-TYPE  319   23
   clus
vv  KRT26 MUTATED KRT26 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D180V7, binary
                 cls
clus                0   1
  KRT26 MUTATED     4   5
  KRT26 WILD-TYPE 255 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT26 MUTATED      4    5
  KRT26 WILD-TYPE  255  216
        clus
vv       KRT26 MUTATED KRT26 WILD-TYPE
  FEMALE             4             255
  MALE               5             216
[1] 2 2
[1] FALSE
D180V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KRT26 MUTATED                            0                                 0
  KRT26 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KRT26 MUTATED                                                    7
  KRT26 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KRT26 MUTATED                                            0
  KRT26 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KRT26 MUTATED                                               1
  KRT26 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KRT26 MUTATED                                0
  KRT26 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KRT26 MUTATED                                    0
  KRT26 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KRT26 MUTATED                              0                             1
  KRT26 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KRT26 MUTATED                                               0
  KRT26 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KRT26 MUTATED                              0
  KRT26 WILD-TYPE                            9
D180V9, multiclass
                                                    clus
vv                                                   KRT26 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   KRT26 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V10, binary
                 cls
clus                0   1
  KRT26 MUTATED     0   9
  KRT26 WILD-TYPE  20 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT26 MUTATED      0    9
  KRT26 WILD-TYPE   20  451
     clus
vv    KRT26 MUTATED KRT26 WILD-TYPE
  NO              0              20
  YES             9             451
[1] 2 2
[1] FALSE
D180V11, continuous
D180V12, continuous
                 vv
clus               R0  R1  R2  RX
  KRT26 MUTATED     8   0   0   0
  KRT26 WILD-TYPE 302  11   4  25
D180V13, multiclass
    clus
vv   KRT26 MUTATED KRT26 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT26 MUTATED                                  0     0
  KRT26 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT26 MUTATED                           2     6
  KRT26 WILD-TYPE                        27   371
D180V14, multiclass
                                  clus
vv                                 KRT26 MUTATED KRT26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V15, binary
                 cls
clus                0   1
  KRT26 MUTATED     0   7
  KRT26 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT26 MUTATED      0    7
  KRT26 WILD-TYPE    6  342
                        clus
vv                       KRT26 MUTATED KRT26 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(181) Variable = CALCRL MUTATION ANALYSIS
D181V1, survival
                  sevent
clus2                0   1
  CALCRL MUTATED     8   3
  CALCRL WILD-TYPE 307 138
  CALCRL MUTATED CALCRL WILD-TYPE 
              11              445 
  CALCRL MUTATED CALCRL WILD-TYPE 
               3              138 
$`CALCRL MUTATED`
TCGA-05-4424 TCGA-05-5428 TCGA-44-8117 TCGA-55-6968 TCGA-55-7994 TCGA-78-7220 
       30.02        22.03        12.66        42.51        19.82        26.53 
TCGA-86-8279 TCGA-86-8358 TCGA-99-8028 TCGA-MP-A4T8 TCGA-NJ-A4YF 
       15.85        21.47        36.76         5.29        71.05 

$`CALCRL WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        17.59        23.64         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
       18.64         0.53         6.48        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.65        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 
       18.67        20.68        24.56        34.85         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG 
       11.05        14.66        14.10        19.13        73.91        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CALCRL MUTATED CALCRL WILD-TYPE 
            5.29             0.00 
  CALCRL MUTATED CALCRL WILD-TYPE 
           71.05           223.96 
  CALCRL MUTATED CALCRL WILD-TYPE 
           22.03            17.75 
[1] "5.3 - 71.0 (22.0)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.4"
D181V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CALCRL MUTATED         0        2        4         2         2          2
  CALCRL WILD-TYPE       4      121      129        44        65         68
                  vv
clus               STAGE IIIB STAGE IV
  CALCRL MUTATED            0        1
  CALCRL WILD-TYPE         11       24
D181V3, multiclass
            clus
vv           CALCRL MUTATED CALCRL WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                4              129
  STAGE IIA               2               44
  STAGE IIB               2               65
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of 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     4   6   3   0
  CALCRL WILD-TYPE 151 255  40  18
D181V4, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  T1              4              151
  T2              6              255
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  CALCRL MUTATED     9   2     2
  CALCRL WILD-TYPE 298  87    70
D181V5, multiclass
       clus
vv      CALCRL MUTATED CALCRL WILD-TYPE
  N0                 9              298
  N1                 2               87
  N2+N3              2               70
[1] 3 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
  CALCRL MUTATED    11   1
  CALCRL WILD-TYPE 316  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED     11    1
  CALCRL WILD-TYPE  316   22
   clus
vv  CALCRL MUTATED CALCRL WILD-TYPE
  0             11              316
  1              1               22
[1] 2 2
[1] FALSE
D181V7, binary
                  cls
clus                 0   1
  CALCRL MUTATED     4   9
  CALCRL WILD-TYPE 255 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      4    9
  CALCRL WILD-TYPE  255  212
        clus
vv       CALCRL MUTATED CALCRL WILD-TYPE
  FEMALE              4              255
  MALE                9              212
[1] 2 2
[1] FALSE
D181V8, continuous
[1] "Remove cluster labels:" "CALCRL MUTATED"        
clus
  CALCRL MUTATED CALCRL WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8281       TCGA-86-8359 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"CALCRL WILD-TYPE" "CALCRL WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CALCRL MUTATED                            0                                 5
  CALCRL WILD-TYPE                         18                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CALCRL MUTATED                                                    8
  CALCRL WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CALCRL MUTATED                                            0
  CALCRL WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CALCRL MUTATED                                               0
  CALCRL WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CALCRL MUTATED                                0
  CALCRL WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CALCRL MUTATED                                    0
  CALCRL WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CALCRL MUTATED                              0                             0
  CALCRL WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CALCRL MUTATED                                               0
  CALCRL WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CALCRL MUTATED                              0
  CALCRL WILD-TYPE                            9
D181V9, multiclass
                                                    clus
vv                                                   CALCRL MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CALCRL WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V10, binary
                  cls
clus                 0   1
  CALCRL MUTATED     1  12
  CALCRL WILD-TYPE  19 448
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      1   12
  CALCRL WILD-TYPE   19  448
     clus
vv    CALCRL MUTATED CALCRL WILD-TYPE
  NO               1               19
  YES             12              448
[1] 2 2
[1] FALSE
D181V11, continuous
D181V12, continuous
                  vv
clus                R0  R1  R2  RX
  CALCRL MUTATED     8   1   0   1
  CALCRL WILD-TYPE 302  10   4  24
D181V13, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  R0              8              302
  R1              1               10
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CALCRL MUTATED                                  0     0
  CALCRL WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CALCRL MUTATED                           2     7
  CALCRL WILD-TYPE                        27   370
D181V14, multiclass
                                  clus
vv                                 CALCRL MUTATED CALCRL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V15, binary
                  cls
clus                 0   1
  CALCRL MUTATED     0   8
  CALCRL WILD-TYPE   6 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      0    8
  CALCRL WILD-TYPE    6  341
                        clus
vv                       CALCRL MUTATED CALCRL WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              341
[1] 2 2
[1] FALSE

Clustering(182) Variable = STRN3 MUTATION ANALYSIS
D182V1, survival
                 sevent
clus2               0   1
  STRN3 MUTATED     7   3
  STRN3 WILD-TYPE 308 138
  STRN3 MUTATED STRN3 WILD-TYPE 
             10             446 
  STRN3 MUTATED STRN3 WILD-TYPE 
              3             138 
$`STRN3 MUTATED`
TCGA-50-5049 TCGA-55-7903 TCGA-55-8205 TCGA-69-7765 TCGA-69-7979 TCGA-78-7150 
       70.55        18.64         1.08         5.42         2.93        21.90 
TCGA-78-7152 TCGA-78-7155 TCGA-86-7711 TCGA-97-A4M5 
       39.52        38.50        34.39        20.84 

$`STRN3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       22.68        13.61         7.56         6.05         2.30        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 
       27.16         5.69        19.27        20.58        35.93        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        17.75        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  STRN3 MUTATED STRN3 WILD-TYPE 
           1.08            0.00 
  STRN3 MUTATED STRN3 WILD-TYPE 
          70.55          223.96 
  STRN3 MUTATED STRN3 WILD-TYPE 
         21.370          17.835 
[1] "1.1 - 70.5 (21.4)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D182V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STRN3 MUTATED         0        3        3         1         2          0
  STRN3 WILD-TYPE       4      120      130        45        65         70
                 vv
clus              STAGE IIIB STAGE IV
  STRN3 MUTATED            0        1
  STRN3 WILD-TYPE         11       24
D182V3, multiclass
            clus
vv           STRN3 MUTATED STRN3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               3             130
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STRN3 MUTATED     2   7   0   1
  STRN3 WILD-TYPE 153 254  43  17
D182V4, multiclass
    clus
vv   STRN3 MUTATED STRN3 WILD-TYPE
  T1             2             153
  T2             7             254
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  STRN3 MUTATED     8   2     0
  STRN3 WILD-TYPE 299  87    72
D182V5, multiclass
       clus
vv      STRN3 MUTATED STRN3 WILD-TYPE
  N0                8             299
  N1                2              87
  N2+N3             0              72
[1] 3 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
  STRN3 MUTATED     7   0
  STRN3 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRN3 MUTATED      7    0
  STRN3 WILD-TYPE  320   23
   clus
vv  STRN3 MUTATED STRN3 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D182V7, binary
                 cls
clus                0   1
  STRN3 MUTATED     2   8
  STRN3 WILD-TYPE 257 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRN3 MUTATED      2    8
  STRN3 WILD-TYPE  257  213
        clus
vv       STRN3 MUTATED STRN3 WILD-TYPE
  FEMALE             2             257
  MALE               8             213
[1] 2 2
[1] FALSE
D182V8, continuous
[1] "Remove cluster labels:" "STRN3 MUTATED"         
clus
  STRN3 MUTATED STRN3 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8208 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7713      TCGA-86-7714 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"STRN3 WILD-TYPE" "STRN3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STRN3 MUTATED                            1                                 3
  STRN3 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STRN3 MUTATED                                                    6
  STRN3 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STRN3 MUTATED                                            0
  STRN3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STRN3 MUTATED                                               0
  STRN3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STRN3 MUTATED                                0
  STRN3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STRN3 MUTATED                                    0
  STRN3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STRN3 MUTATED                              0                             0
  STRN3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STRN3 MUTATED                                               0
  STRN3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STRN3 MUTATED                              0
  STRN3 WILD-TYPE                            9
D182V9, multiclass
                                                    clus
vv                                                   STRN3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STRN3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V10, binary
                 cls
clus                0   1
  STRN3 MUTATED     1   9
  STRN3 WILD-TYPE  19 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRN3 MUTATED      1    9
  STRN3 WILD-TYPE   19  451
     clus
vv    STRN3 MUTATED STRN3 WILD-TYPE
  NO              1              19
  YES             9             451
[1] 2 2
[1] FALSE
D182V11, continuous
D182V12, continuous
                 vv
clus               R0  R1  R2  RX
  STRN3 MUTATED     6   0   0   0
  STRN3 WILD-TYPE 304  11   4  25
D182V13, multiclass
    clus
vv   STRN3 MUTATED STRN3 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STRN3 MUTATED                                  0     0
  STRN3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STRN3 MUTATED                           1     9
  STRN3 WILD-TYPE                        28   368
D182V14, multiclass
                                  clus
vv                                 STRN3 MUTATED STRN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V15, binary
                 cls
clus                0   1
  STRN3 MUTATED     1   6
  STRN3 WILD-TYPE   5 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRN3 MUTATED      1    6
  STRN3 WILD-TYPE    5  343
                        clus
vv                       STRN3 MUTATED STRN3 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(183) Variable = RPS16 MUTATION ANALYSIS
D183V1, survival
                 sevent
clus2               0   1
  RPS16 MUTATED     2   1
  RPS16 WILD-TYPE 313 140
  RPS16 MUTATED RPS16 WILD-TYPE 
              3             453 
  RPS16 MUTATED RPS16 WILD-TYPE 
              1             140 
$`RPS16 MUTATED`
TCGA-53-7624 TCGA-55-7576 TCGA-86-6851 
       34.29         1.32         5.88 

$`RPS16 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        25.61         7.59        27.25        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        3.12        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  RPS16 MUTATED RPS16 WILD-TYPE 
           1.32            0.00 
  RPS16 MUTATED RPS16 WILD-TYPE 
          34.29          223.96 
  RPS16 MUTATED RPS16 WILD-TYPE 
           5.88           18.08 
[1] "1.3 - 34.3 (5.9)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.9"
D183V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RPS16 MUTATED         0        0        1         1         0          0
  RPS16 WILD-TYPE       4      123      132        45        67         70
                 vv
clus              STAGE IIIB STAGE IV
  RPS16 MUTATED            0        1
  RPS16 WILD-TYPE         11       24
D183V3, multiclass
            clus
vv           RPS16 MUTATED RPS16 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               1             132
  STAGE IIA              1              45
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RPS16 MUTATED     1   2   0   0
  RPS16 WILD-TYPE 154 259  43  18
D183V4, multiclass
    clus
vv   RPS16 MUTATED RPS16 WILD-TYPE
  T1             1             154
  T2             2             259
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  RPS16 MUTATED     2   1     0
  RPS16 WILD-TYPE 305  88    72
D183V5, multiclass
       clus
vv      RPS16 MUTATED RPS16 WILD-TYPE
  N0                2             305
  N1                1              88
  N2+N3             0              72
[1] 3 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
  RPS16 MUTATED     2   1
  RPS16 WILD-TYPE 325  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS16 MUTATED      2    1
  RPS16 WILD-TYPE  325   22
   clus
vv  RPS16 MUTATED RPS16 WILD-TYPE
  0             2             325
  1             1              22
[1] 2 2
[1] FALSE
D183V7, binary
                 cls
clus                0   1
  RPS16 MUTATED     2   1
  RPS16 WILD-TYPE 257 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS16 MUTATED      2    1
  RPS16 WILD-TYPE  257  220
        clus
vv       RPS16 MUTATED RPS16 WILD-TYPE
  FEMALE             2             257
  MALE               1             220
[1] 2 2
[1] FALSE
D183V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RPS16 MUTATED                            0                                 1
  RPS16 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RPS16 MUTATED                                                    2
  RPS16 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RPS16 MUTATED                                            0
  RPS16 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RPS16 MUTATED                                               0
  RPS16 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RPS16 MUTATED                                0
  RPS16 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RPS16 MUTATED                                    0
  RPS16 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RPS16 MUTATED                              0                             0
  RPS16 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RPS16 MUTATED                                               0
  RPS16 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RPS16 MUTATED                              0
  RPS16 WILD-TYPE                            9
D183V9, multiclass
                                                    clus
vv                                                   RPS16 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   RPS16 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V10, binary
                 cls
clus                0   1
  RPS16 MUTATED     0   3
  RPS16 WILD-TYPE  20 457
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS16 MUTATED      0    3
  RPS16 WILD-TYPE   20  457
     clus
vv    RPS16 MUTATED RPS16 WILD-TYPE
  NO              0              20
  YES             3             457
[1] 2 2
[1] FALSE
D183V11, continuous
[1] "Remove cluster labels:" "RPS16 MUTATED"         
clus
  RPS16 MUTATED RPS16 WILD-TYPE 
              2             331 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4396 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4397      TCGA-05-4398      TCGA-05-4405      TCGA-05-4410 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4415      TCGA-05-4417      TCGA-05-4418      TCGA-05-4420 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4422      TCGA-05-4424      TCGA-05-4425      TCGA-05-4426 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4430      TCGA-05-4432      TCGA-05-4433 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4434      TCGA-05-5420      TCGA-05-5423      TCGA-05-5425 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-5428      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-38-4625      TCGA-38-4626      TCGA-38-4629      TCGA-38-4631 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-38-4632      TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-3396      TCGA-44-3398      TCGA-44-3918 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-4112      TCGA-44-5643      TCGA-44-5644      TCGA-44-5645 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6145      TCGA-44-6146      TCGA-44-6148 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-6774      TCGA-44-6775      TCGA-44-6776      TCGA-44-6777 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-6778      TCGA-44-6779      TCGA-44-7659      TCGA-44-7660 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-7661      TCGA-44-7662      TCGA-44-7667      TCGA-44-7669 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-7670      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4490      TCGA-49-4494 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4507      TCGA-49-4510 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-4514      TCGA-49-6742      TCGA-49-6743      TCGA-49-6744 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-6745      TCGA-49-6761      TCGA-49-6767      TCGA-50-5051 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-50-5072      TCGA-50-5931      TCGA-50-5939      TCGA-50-5941 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-50-5942      TCGA-50-6590      TCGA-50-7109      TCGA-50-8457 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-50-8459      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-6543      TCGA-55-6971      TCGA-55-6983      TCGA-55-6985 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7281      TCGA-55-7283      TCGA-55-7574      TCGA-55-7724 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7903 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7907      TCGA-55-7910      TCGA-55-7911      TCGA-55-7914 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7994      TCGA-55-7995      TCGA-55-8089      TCGA-55-8092 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8094      TCGA-55-8096      TCGA-55-8097      TCGA-55-8203 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8208      TCGA-55-8299      TCGA-55-8301 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8302      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8614      TCGA-55-8615      TCGA-55-8620 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A491      TCGA-55-A492      TCGA-55-A493 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG      TCGA-62-8398 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-62-A46S      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-64-1676      TCGA-64-1677      TCGA-64-1679      TCGA-64-5774 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-64-5815      TCGA-69-7761      TCGA-69-7763      TCGA-69-7764 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-69-7973      TCGA-69-7974      TCGA-69-7978      TCGA-69-7979 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-69-7980      TCGA-69-8253      TCGA-69-8254      TCGA-69-8255 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4658      TCGA-73-4659      TCGA-73-4662 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4668      TCGA-73-4670      TCGA-73-4675 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-75-5122      TCGA-75-5125 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-75-5126      TCGA-75-6203      TCGA-75-6206      TCGA-75-6207 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-75-6211      TCGA-75-6214      TCGA-75-7027      TCGA-75-7031 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-80-5608      TCGA-80-5611      TCGA-83-5908      TCGA-86-7701 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7714      TCGA-86-7954      TCGA-86-8054 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8358      TCGA-86-8359      TCGA-86-8669 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8673      TCGA-86-8674      TCGA-91-6829      TCGA-91-6830 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-91-6835      TCGA-91-6836      TCGA-91-6840      TCGA-91-6849 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-91-7771      TCGA-91-8499      TCGA-91-A4BC      TCGA-93-7347 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-95-7039      TCGA-95-7043      TCGA-95-7562      TCGA-95-7944 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-95-7947      TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547      TCGA-97-7552 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7937      TCGA-97-7938 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-97-7941      TCGA-97-8171      TCGA-97-8172      TCGA-97-8174 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-97-8176      TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-97-A4M1      TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025      TCGA-99-8028 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-99-8032      TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-L4-A4E5      TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY      TCGA-MP-A4T2 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7      TCGA-MP-A4T8 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TD 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YF      TCGA-NJ-A4YG 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ      TCGA-NJ-A55A 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
D183V12, continuous
                 vv
clus               R0  R1  R2  RX
  RPS16 MUTATED     2   0   0   0
  RPS16 WILD-TYPE 308  11   4  25
D183V13, multiclass
[1] "Remove cluster labels:" "RPS16 MUTATED"         
clus
  RPS16 MUTATED RPS16 WILD-TYPE 
              2             348 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4395 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4396      TCGA-05-4397      TCGA-05-4398      TCGA-05-4402 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4403      TCGA-05-4405      TCGA-05-4410      TCGA-05-4415 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4417      TCGA-05-4418      TCGA-05-4420      TCGA-05-4422 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4424      TCGA-05-4425      TCGA-05-4426      TCGA-05-4427 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-4430      TCGA-05-4432      TCGA-05-4433      TCGA-05-4434 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-5420      TCGA-05-5423      TCGA-05-5425      TCGA-05-5428 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-05-5429      TCGA-05-5715      TCGA-35-4122      TCGA-35-4123 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-4627 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-38-4628      TCGA-38-4629      TCGA-38-4630      TCGA-38-4631 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-38-4632      TCGA-38-6178      TCGA-38-7271      TCGA-38-A44F 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2661      TCGA-44-2665      TCGA-44-3396 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-3919      TCGA-44-4112 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6148      TCGA-44-6775      TCGA-44-A479 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47G      TCGA-44-A4SU 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4488      TCGA-49-4494 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-4501      TCGA-49-4505      TCGA-49-4506      TCGA-49-4507 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-4510      TCGA-49-4512      TCGA-49-4514      TCGA-49-6742 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-49-6744      TCGA-49-6761      TCGA-49-6767      TCGA-50-5051 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-50-5055      TCGA-50-5066      TCGA-50-5931      TCGA-50-5942 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-50-5944      TCGA-50-6593      TCGA-50-6597      TCGA-50-6673 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-50-8460      TCGA-53-7626      TCGA-53-A4EZ      TCGA-55-1592 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-5899      TCGA-55-6642      TCGA-55-6970      TCGA-55-6971 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-6972      TCGA-55-6980      TCGA-55-6981      TCGA-55-6983 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-6985      TCGA-55-7281      TCGA-55-7284      TCGA-55-7570 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7724      TCGA-55-7725      TCGA-55-7726 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7727      TCGA-55-7728      TCGA-55-7815      TCGA-55-7903 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7907      TCGA-55-7910      TCGA-55-7911      TCGA-55-7914 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-7994      TCGA-55-7995      TCGA-55-8085      TCGA-55-8087 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8090      TCGA-55-8091      TCGA-55-8092 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8094      TCGA-55-8097      TCGA-55-8203      TCGA-55-8204 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8206      TCGA-55-8207      TCGA-55-8208 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8299      TCGA-55-8301      TCGA-55-8302      TCGA-55-8505 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8506      TCGA-55-8507      TCGA-55-8508      TCGA-55-8510 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8513      TCGA-55-8514 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8614      TCGA-55-8615      TCGA-55-8616      TCGA-55-8619 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-64-1676      TCGA-64-1677      TCGA-64-1679      TCGA-64-1681 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-64-5774      TCGA-64-5775      TCGA-64-5778      TCGA-64-5779 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-64-5781      TCGA-64-5815      TCGA-67-3771      TCGA-67-3773 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-67-4679      TCGA-67-6215      TCGA-67-6216      TCGA-67-6217 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4658      TCGA-73-4659 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-4677      TCGA-73-7498 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-73-7499      TCGA-75-5122      TCGA-75-5125      TCGA-75-5126 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-75-5146      TCGA-75-5147      TCGA-75-6203      TCGA-75-6205 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-75-6206      TCGA-75-6207      TCGA-75-6211      TCGA-75-6212 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7030 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7143      TCGA-78-7145      TCGA-78-7146 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7147      TCGA-78-7148      TCGA-78-7149      TCGA-78-7150 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7152      TCGA-78-7153      TCGA-78-7154      TCGA-78-7155 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7156      TCGA-78-7158      TCGA-78-7159      TCGA-78-7160 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7161      TCGA-78-7162      TCGA-78-7163      TCGA-78-7166 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7167      TCGA-78-7220      TCGA-78-7535      TCGA-78-7536 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7537      TCGA-78-7539      TCGA-78-7540      TCGA-78-7542 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-7633      TCGA-78-8640      TCGA-78-8648      TCGA-78-8655 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-78-8660      TCGA-78-8662      TCGA-80-5607      TCGA-80-5608 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-80-5611      TCGA-83-5908      TCGA-86-6562      TCGA-86-7701 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7713      TCGA-86-7714      TCGA-86-7953 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8054      TCGA-86-8055 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8075 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8585      TCGA-86-8668 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8671      TCGA-86-8672      TCGA-86-8673 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-91-6828      TCGA-91-6829      TCGA-91-6835      TCGA-91-6840 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-91-A4BD      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JP      TCGA-93-A4JQ 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-95-8039      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-97-7546 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-97-7554      TCGA-97-7938      TCGA-97-7941      TCGA-97-8176 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-99-8028      TCGA-99-8032      TCGA-99-8033      TCGA-J2-A4AD 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-J2-A4AE      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4T8      TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
     TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YQ 
"RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" "RPS16 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS16 MUTATED                                  0     0
  RPS16 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RPS16 MUTATED                           1     2
  RPS16 WILD-TYPE                        28   375
D183V14, multiclass
                                  clus
vv                                 RPS16 MUTATED RPS16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        2             375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V15, binary
                 cls
clus                0   1
  RPS16 MUTATED     1   2
  RPS16 WILD-TYPE   5 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS16 MUTATED      1    2
  RPS16 WILD-TYPE    5  347
                        clus
vv                       RPS16 MUTATED RPS16 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             2             347
[1] 2 2
[1] FALSE

Clustering(184) Variable = NPR1 MUTATION ANALYSIS
D184V1, survival
                sevent
clus2              0   1
  NPR1 MUTATED     9   3
  NPR1 WILD-TYPE 306 138
  NPR1 MUTATED NPR1 WILD-TYPE 
            12            444 
  NPR1 MUTATED NPR1 WILD-TYPE 
             3            138 
$`NPR1 MUTATED`
TCGA-05-4398 TCGA-44-7660 TCGA-44-7670 TCGA-50-5930 TCGA-50-5931 TCGA-55-7994 
       47.05        19.46        29.00         9.27        14.27        19.82 
TCGA-55-8089 TCGA-64-5778 TCGA-69-7979 TCGA-73-4668 TCGA-86-7701 TCGA-MP-A4TI 
        3.29        42.90         2.93        15.35        31.13        14.10 

$`NPR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        14.60        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       31.04        49.28         8.22        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  NPR1 MUTATED NPR1 WILD-TYPE 
          2.93           0.00 
  NPR1 MUTATED NPR1 WILD-TYPE 
         47.05         223.96 
  NPR1 MUTATED NPR1 WILD-TYPE 
        17.405         18.030 
[1] "2.9 - 47.0 (17.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D184V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NPR1 MUTATED         0        2        4         2         3          1
  NPR1 WILD-TYPE       4      121      129        44        64         69
                vv
clus             STAGE IIIB STAGE IV
  NPR1 MUTATED            1        1
  NPR1 WILD-TYPE         10       24
D184V3, multiclass
            clus
vv           NPR1 MUTATED NPR1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              4            129
  STAGE IIA             2             44
  STAGE IIB             3             64
  STAGE IIIA            1             69
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NPR1 MUTATED     3   9   1   1
  NPR1 WILD-TYPE 152 252  42  17
D184V4, multiclass
    clus
vv   NPR1 MUTATED NPR1 WILD-TYPE
  T1            3            152
  T2            9            252
  T3            1             42
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  NPR1 MUTATED     8   4     2
  NPR1 WILD-TYPE 299  85    70
D184V5, multiclass
       clus
vv      NPR1 MUTATED NPR1 WILD-TYPE
  N0               8            299
  N1               4             85
  N2+N3            2             70
[1] 3 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
  NPR1 MUTATED    10   1
  NPR1 WILD-TYPE 317  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR1 MUTATED     10    1
  NPR1 WILD-TYPE  317   22
   clus
vv  NPR1 MUTATED NPR1 WILD-TYPE
  0           10            317
  1            1             22
[1] 2 2
[1] FALSE
D184V7, binary
                cls
clus               0   1
  NPR1 MUTATED     7   7
  NPR1 WILD-TYPE 252 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR1 MUTATED      7    7
  NPR1 WILD-TYPE  252  214
        clus
vv       NPR1 MUTATED NPR1 WILD-TYPE
  FEMALE            7            252
  MALE              7            214
[1] 2 2
[1] FALSE
D184V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NPR1 MUTATED                            1                                 2
  NPR1 WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NPR1 MUTATED                                                    9
  NPR1 WILD-TYPE                                                285
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NPR1 MUTATED                                            0
  NPR1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NPR1 MUTATED                                               1
  NPR1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  NPR1 MUTATED                                0
  NPR1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  NPR1 MUTATED                                    1
  NPR1 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NPR1 MUTATED                              0                             0
  NPR1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NPR1 MUTATED                                               0
  NPR1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  NPR1 MUTATED                              0
  NPR1 WILD-TYPE                            9
D184V9, multiclass
                                                    clus
vv                                                   NPR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   NPR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V10, binary
                cls
clus               0   1
  NPR1 MUTATED     1  13
  NPR1 WILD-TYPE  19 447
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR1 MUTATED      1   13
  NPR1 WILD-TYPE   19  447
     clus
vv    NPR1 MUTATED NPR1 WILD-TYPE
  NO             1             19
  YES           13            447
[1] 2 2
[1] FALSE
D184V11, continuous
D184V12, continuous
                vv
clus              R0  R1  R2  RX
  NPR1 MUTATED    10   0   0   0
  NPR1 WILD-TYPE 300  11   4  25
D184V13, multiclass
    clus
vv   NPR1 MUTATED NPR1 WILD-TYPE
  R0           10            300
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NPR1 MUTATED                                  1     0
  NPR1 WILD-TYPE                                0     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NPR1 MUTATED                           0    10
  NPR1 WILD-TYPE                        29   367
D184V14, multiclass
                                  clus
vv                                 NPR1 MUTATED NPR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                      10            367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V15, binary
                cls
clus               0   1
  NPR1 MUTATED     1  10
  NPR1 WILD-TYPE   5 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR1 MUTATED      1   10
  NPR1 WILD-TYPE    5  339
                        clus
vv                       NPR1 MUTATED NPR1 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(185) Variable = KARS MUTATION ANALYSIS
D185V1, survival
                sevent
clus2              0   1
  KARS MUTATED     5   1
  KARS WILD-TYPE 310 140
  KARS MUTATED KARS WILD-TYPE 
             6            450 
  KARS MUTATED KARS WILD-TYPE 
             1            140 
$`KARS MUTATED`
TCGA-05-5425 TCGA-44-7670 TCGA-53-A4EZ TCGA-55-8089 TCGA-78-7146 TCGA-86-8073 
       29.00        29.00         9.21         3.29         5.69        24.33 

$`KARS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  KARS MUTATED KARS WILD-TYPE 
          3.29           0.00 
  KARS MUTATED KARS WILD-TYPE 
         29.00         223.96 
  KARS MUTATED KARS WILD-TYPE 
         16.77          18.03 
[1] "3.3 - 29.0 (16.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D185V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KARS MUTATED         0        1        2         2         1          1
  KARS WILD-TYPE       4      122      131        44        66         69
                vv
clus             STAGE IIIB STAGE IV
  KARS MUTATED            0        0
  KARS WILD-TYPE         11       25
D185V3, multiclass
            clus
vv           KARS MUTATED KARS WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            131
  STAGE IIA             2             44
  STAGE IIB             1             66
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KARS MUTATED     2   5   0   0
  KARS WILD-TYPE 153 256  43  18
D185V4, multiclass
    clus
vv   KARS MUTATED KARS WILD-TYPE
  T1            2            153
  T2            5            256
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  KARS MUTATED     3   3     1
  KARS WILD-TYPE 304  86    71
D185V5, multiclass
       clus
vv      KARS MUTATED KARS WILD-TYPE
  N0               3            304
  N1               3             86
  N2+N3            1             71
[1] 3 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
  KARS MUTATED     6   0
  KARS WILD-TYPE 321  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  KARS MUTATED      6    0
  KARS WILD-TYPE  321   23
   clus
vv  KARS MUTATED KARS WILD-TYPE
  0            6            321
  1            0             23
[1] 2 2
[1] FALSE
D185V7, binary
                cls
clus               0   1
  KARS MUTATED     2   5
  KARS WILD-TYPE 257 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  KARS MUTATED      2    5
  KARS WILD-TYPE  257  216
        clus
vv       KARS MUTATED KARS WILD-TYPE
  FEMALE            2            257
  MALE              5            216
[1] 2 2
[1] FALSE
D185V8, continuous
[1] "Remove cluster labels:" "KARS MUTATED"          
clus
  KARS MUTATED KARS WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-55-7283 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-55-7573     TCGA-55-7725     TCGA-55-7910     TCGA-55-7914 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-55-8096     TCGA-55-8205     TCGA-55-8208     TCGA-55-8507 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-55-8508     TCGA-55-8511     TCGA-55-8512     TCGA-55-8619 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5778     TCGA-69-7974 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-69-8254     TCGA-71-6725     TCGA-71-8520     TCGA-73-4659 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4676 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8055     TCGA-86-8056 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" "KARS WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"KARS WILD-TYPE" "KARS WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KARS MUTATED                            1                                 2
  KARS WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KARS MUTATED                                                    2
  KARS WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KARS MUTATED                                            0
  KARS WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KARS MUTATED                                               1
  KARS WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  KARS MUTATED                                0
  KARS WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  KARS MUTATED                                    0
  KARS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KARS MUTATED                              0                             0
  KARS WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KARS MUTATED                                               1
  KARS WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  KARS MUTATED                              0
  KARS WILD-TYPE                            9
D185V9, multiclass
                                                    clus
vv                                                   KARS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   KARS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V10, binary
                cls
clus               0   1
  KARS MUTATED     0   7
  KARS WILD-TYPE  20 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  KARS MUTATED      0    7
  KARS WILD-TYPE   20  453
     clus
vv    KARS MUTATED KARS WILD-TYPE
  NO             0             20
  YES            7            453
[1] 2 2
[1] FALSE
D185V11, continuous
D185V12, continuous
                vv
clus              R0  R1  R2  RX
  KARS MUTATED     5   0   0   1
  KARS WILD-TYPE 305  11   4  24
D185V13, multiclass
    clus
vv   KARS MUTATED KARS WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KARS MUTATED                                  0     0
  KARS WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KARS MUTATED                           0     5
  KARS WILD-TYPE                        29   372
D185V14, multiclass
                                  clus
vv                                 KARS MUTATED KARS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V15, binary
                cls
clus               0   1
  KARS MUTATED     2   2
  KARS WILD-TYPE   4 347
[1] "tbl2"
                cls
clus             [,1] [,2]
  KARS MUTATED      2    2
  KARS WILD-TYPE    4  347
                        clus
vv                       KARS MUTATED KARS WILD-TYPE
  HISPANIC OR LATINO                2              4
  NOT HISPANIC OR LATINO            2            347
[1] 2 2
[1] FALSE

Clustering(186) Variable = FRMD6 MUTATION ANALYSIS
D186V1, survival
                 sevent
clus2               0   1
  FRMD6 MUTATED    11   3
  FRMD6 WILD-TYPE 304 138
  FRMD6 MUTATED FRMD6 WILD-TYPE 
             14             442 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
              3             138 
$`FRMD6 MUTATED`
TCGA-05-4398 TCGA-05-4418 TCGA-05-5428 TCGA-44-6774 TCGA-49-6743 TCGA-50-5045 
       47.05         9.01        22.03        21.63        12.13        71.47 
TCGA-55-7576 TCGA-55-8203 TCGA-69-7979 TCGA-78-7161 TCGA-78-7220 TCGA-83-5908 
        1.32        17.98         2.93         7.07        26.53        27.09 
TCGA-86-8073 TCGA-97-7554 
       24.33        25.48 

$`FRMD6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
       15.02         4.96        29.00         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       14.63        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         3.12        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
       32.09         5.88        64.90        22.29       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  FRMD6 MUTATED FRMD6 WILD-TYPE 
           1.32            0.00 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
          71.47          223.96 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
         21.830          17.835 
[1] "1.3 - 71.5 (21.8)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.4"
D186V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FRMD6 MUTATED         0        2        4         1         1          5
  FRMD6 WILD-TYPE       4      121      129        45        66         65
                 vv
clus              STAGE IIIB STAGE IV
  FRMD6 MUTATED            1        0
  FRMD6 WILD-TYPE         10       25
D186V3, multiclass
            clus
vv           FRMD6 MUTATED FRMD6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             5              65
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FRMD6 MUTATED     5   6   2   1
  FRMD6 WILD-TYPE 150 255  41  17
D186V4, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  T1             5             150
  T2             6             255
  T3             2              41
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  FRMD6 MUTATED     6   2     6
  FRMD6 WILD-TYPE 301  87    66
D186V5, multiclass
       clus
vv      FRMD6 MUTATED FRMD6 WILD-TYPE
  N0                6             301
  N1                2              87
  N2+N3             6              66
[1] 3 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
  FRMD6 MUTATED    11   0
  FRMD6 WILD-TYPE 316  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED     11    0
  FRMD6 WILD-TYPE  316   23
   clus
vv  FRMD6 MUTATED FRMD6 WILD-TYPE
  0            11             316
  1             0              23
[1] 2 2
[1] FALSE
D186V7, binary
                 cls
clus                0   1
  FRMD6 MUTATED    10   4
  FRMD6 WILD-TYPE 249 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED     10    4
  FRMD6 WILD-TYPE  249  217
        clus
vv       FRMD6 MUTATED FRMD6 WILD-TYPE
  FEMALE            10             249
  MALE               4             217
[1] 2 2
[1] FALSE
D186V8, continuous
[1] "Remove cluster labels:" "FRMD6 MUTATED"         
clus
  FRMD6 MUTATED FRMD6 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-75-5122      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" "FRMD6 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FRMD6 MUTATED                            1                                 5
  FRMD6 WILD-TYPE                         17                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FRMD6 MUTATED                                                    5
  FRMD6 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FRMD6 MUTATED                                            0
  FRMD6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FRMD6 MUTATED                                               1
  FRMD6 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FRMD6 MUTATED                                1
  FRMD6 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FRMD6 MUTATED                                    0
  FRMD6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FRMD6 MUTATED                              0                             1
  FRMD6 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FRMD6 MUTATED                                               0
  FRMD6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FRMD6 MUTATED                              0
  FRMD6 WILD-TYPE                            9
D186V9, multiclass
                                                    clus
vv                                                   FRMD6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FRMD6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V10, binary
                 cls
clus                0   1
  FRMD6 MUTATED     3  11
  FRMD6 WILD-TYPE  17 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      3   11
  FRMD6 WILD-TYPE   17  449
     clus
vv    FRMD6 MUTATED FRMD6 WILD-TYPE
  NO              3              17
  YES            11             449
[1] 2 2
[1] FALSE
D186V11, continuous
D186V12, continuous
                 vv
clus               R0  R1  R2  RX
  FRMD6 MUTATED     9   1   0   0
  FRMD6 WILD-TYPE 301  10   4  25
D186V13, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  R0             9             301
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRMD6 MUTATED                                  0     0
  FRMD6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FRMD6 MUTATED                           2     9
  FRMD6 WILD-TYPE                        27   368
D186V14, multiclass
                                  clus
vv                                 FRMD6 MUTATED FRMD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V15, binary
                 cls
clus                0   1
  FRMD6 MUTATED     0   8
  FRMD6 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      0    8
  FRMD6 WILD-TYPE    6  341
                        clus
vv                       FRMD6 MUTATED FRMD6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(187) Variable = TMC4 MUTATION ANALYSIS
D187V1, survival
                sevent
clus2              0   1
  TMC4 MUTATED     6   3
  TMC4 WILD-TYPE 309 138
  TMC4 MUTATED TMC4 WILD-TYPE 
             9            447 
  TMC4 MUTATED TMC4 WILD-TYPE 
             3            138 
$`TMC4 MUTATED`
TCGA-38-7271 TCGA-49-6743 TCGA-53-7624 TCGA-55-7815 TCGA-55-8506 TCGA-86-7711 
       26.30        12.13        34.29         1.78         0.36        34.39 
TCGA-86-8673 TCGA-93-8067 TCGA-95-7948 
       14.96         6.12        15.65 

$`TMC4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       44.61        14.73         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
       29.46        29.75        55.89        14.63        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 
       23.18         1.28         1.28         1.12         0.79         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82         9.76         4.18        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.68        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  TMC4 MUTATED TMC4 WILD-TYPE 
          0.36           0.00 
  TMC4 MUTATED TMC4 WILD-TYPE 
         34.39         223.96 
  TMC4 MUTATED TMC4 WILD-TYPE 
         14.96          18.12 
[1] "0.4 - 34.4 (15.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.7"
D187V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TMC4 MUTATED         0        1        4         1         1          1
  TMC4 WILD-TYPE       4      122      129        45        66         69
                vv
clus             STAGE IIIB STAGE IV
  TMC4 MUTATED            0        1
  TMC4 WILD-TYPE         11       24
D187V3, multiclass
            clus
vv           TMC4 MUTATED TMC4 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              4            129
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   6   1   0
  TMC4 WILD-TYPE 153 255  42  18
D187V4, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  T1            2            153
  T2            6            255
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  TMC4 MUTATED     7   1     1
  TMC4 WILD-TYPE 300  88    71
D187V5, multiclass
       clus
vv      TMC4 MUTATED TMC4 WILD-TYPE
  N0               7            300
  N1               1             88
  N2+N3            1             71
[1] 3 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
  TMC4 MUTATED     4   1
  TMC4 WILD-TYPE 323  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      4    1
  TMC4 WILD-TYPE  323   22
   clus
vv  TMC4 MUTATED TMC4 WILD-TYPE
  0            4            323
  1            1             22
[1] 2 2
[1] FALSE
D187V7, binary
                cls
clus               0   1
  TMC4 MUTATED     5   4
  TMC4 WILD-TYPE 254 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      5    4
  TMC4 WILD-TYPE  254  217
        clus
vv       TMC4 MUTATED TMC4 WILD-TYPE
  FEMALE            5            254
  MALE              4            217
[1] 2 2
[1] FALSE
D187V8, continuous
[1] "Remove cluster labels:" "TMC4 MUTATED"          
clus
  TMC4 MUTATED TMC4 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7713 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TMC4 MUTATED                            0                                 1
  TMC4 WILD-TYPE                         18                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TMC4 MUTATED                                                    6
  TMC4 WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TMC4 MUTATED                                            0
  TMC4 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TMC4 MUTATED                                               1
  TMC4 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  TMC4 MUTATED                                1
  TMC4 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  TMC4 MUTATED                                    0
  TMC4 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TMC4 MUTATED                              0                             0
  TMC4 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TMC4 MUTATED                                               0
  TMC4 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  TMC4 MUTATED                              0
  TMC4 WILD-TYPE                            9
D187V9, multiclass
                                                    clus
vv                                                   TMC4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   TMC4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V10, binary
                cls
clus               0   1
  TMC4 MUTATED     0   9
  TMC4 WILD-TYPE  20 451
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      0    9
  TMC4 WILD-TYPE   20  451
     clus
vv    TMC4 MUTATED TMC4 WILD-TYPE
  NO             0             20
  YES            9            451
[1] 2 2
[1] FALSE
D187V11, continuous
D187V12, continuous
                vv
clus              R0  R1  R2  RX
  TMC4 MUTATED     7   0   0   1
  TMC4 WILD-TYPE 303  11   4  24
D187V13, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMC4 MUTATED                                  0     1
  TMC4 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TMC4 MUTATED                           0     7
  TMC4 WILD-TYPE                        29   370
D187V14, multiclass
                                  clus
vv                                 TMC4 MUTATED TMC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V15, binary
                cls
clus               0   1
  TMC4 MUTATED     2   5
  TMC4 WILD-TYPE   4 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      2    5
  TMC4 WILD-TYPE    4  344
                        clus
vv                       TMC4 MUTATED TMC4 WILD-TYPE
  HISPANIC OR LATINO                2              4
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(188) Variable = ARMC3 MUTATION ANALYSIS
D188V1, survival
                 sevent
clus2               0   1
  ARMC3 MUTATED    14   8
  ARMC3 WILD-TYPE 301 133
  ARMC3 MUTATED ARMC3 WILD-TYPE 
             22             434 
  ARMC3 MUTATED ARMC3 WILD-TYPE 
              8             133 
$`ARMC3 MUTATED`
TCGA-05-4249 TCGA-05-4427 TCGA-05-4432 TCGA-44-6774 TCGA-44-8119 TCGA-49-4487 
       50.07        26.01        25.02        21.63         3.25        28.11 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5946 TCGA-50-6590 TCGA-50-7109 TCGA-55-1592 
        9.27        14.27        22.55        42.35        10.13        23.05 
TCGA-55-7281 TCGA-55-8301 TCGA-55-A491 TCGA-55-A4DG TCGA-73-4662 TCGA-73-4677 
        0.59         1.45        20.58        19.99        29.98         1.25 
TCGA-78-8662 TCGA-91-6836 TCGA-97-7941 TCGA-99-8025 
      110.50        13.71         0.72        34.85 

$`ARMC3 WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       21.99        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       29.03        25.12         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 
       34.29        30.54        13.94         9.21        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       70.26         1.74         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40         1.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       20.19         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        1.32         5.39        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        5.95         0.59        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ARMC3 MUTATED ARMC3 WILD-TYPE 
           0.59            0.00 
  ARMC3 MUTATED ARMC3 WILD-TYPE 
         110.50          223.96 
  ARMC3 MUTATED ARMC3 WILD-TYPE 
         21.105          17.835 
[1] "0.6 - 110.5 (21.1)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.2"
D188V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARMC3 MUTATED         0       10        6         0         3          3
  ARMC3 WILD-TYPE       4      113      127        46        64         67
                 vv
clus              STAGE IIIB STAGE IV
  ARMC3 MUTATED            0        0
  ARMC3 WILD-TYPE         11       25
D188V3, multiclass
            clus
vv           ARMC3 MUTATED ARMC3 WILD-TYPE
  STAGE I                0               4
  STAGE IA              10             113
  STAGE IB               6             127
  STAGE IIA              0              46
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARMC3 MUTATED     9  11   2   0
  ARMC3 WILD-TYPE 146 250  41  18
D188V4, multiclass
    clus
vv   ARMC3 MUTATED ARMC3 WILD-TYPE
  T1             9             146
  T2            11             250
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ARMC3 MUTATED    17   2     3
  ARMC3 WILD-TYPE 290  87    69
D188V5, multiclass
       clus
vv      ARMC3 MUTATED ARMC3 WILD-TYPE
  N0               17             290
  N1                2              87
  N2+N3             3              69
[1] 3 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
  ARMC3 MUTATED    16   0
  ARMC3 WILD-TYPE 311  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC3 MUTATED     16    0
  ARMC3 WILD-TYPE  311   23
   clus
vv  ARMC3 MUTATED ARMC3 WILD-TYPE
  0            16             311
  1             0              23
[1] 2 2
[1] FALSE
D188V7, binary
                 cls
clus                0   1
  ARMC3 MUTATED    12  10
  ARMC3 WILD-TYPE 247 211
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC3 MUTATED     12   10
  ARMC3 WILD-TYPE  247  211
        clus
vv       ARMC3 MUTATED ARMC3 WILD-TYPE
  FEMALE            12             247
  MALE              10             211
[1] 2 2
[1] FALSE
D188V8, continuous
[1] "Remove cluster labels:" "ARMC3 MUTATED"         
clus
  ARMC3 MUTATED ARMC3 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4666      TCGA-73-4668 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" "ARMC3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARMC3 MUTATED                            1                                 4
  ARMC3 WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARMC3 MUTATED                                                   17
  ARMC3 WILD-TYPE                                                277
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARMC3 MUTATED                                            0
  ARMC3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARMC3 MUTATED                                               0
  ARMC3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ARMC3 MUTATED                                0
  ARMC3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ARMC3 MUTATED                                    0
  ARMC3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARMC3 MUTATED                              0                             0
  ARMC3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARMC3 MUTATED                                               0
  ARMC3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ARMC3 MUTATED                              0
  ARMC3 WILD-TYPE                            9
D188V9, multiclass
                                                    clus
vv                                                   ARMC3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ARMC3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V10, binary
                 cls
clus                0   1
  ARMC3 MUTATED     2  20
  ARMC3 WILD-TYPE  18 440
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC3 MUTATED      2   20
  ARMC3 WILD-TYPE   18  440
     clus
vv    ARMC3 MUTATED ARMC3 WILD-TYPE
  NO              2              18
  YES            20             440
[1] 2 2
[1] FALSE
D188V11, continuous
D188V12, continuous
                 vv
clus               R0  R1  R2  RX
  ARMC3 MUTATED    15   0   0   0
  ARMC3 WILD-TYPE 295  11   4  25
D188V13, multiclass
    clus
vv   ARMC3 MUTATED ARMC3 WILD-TYPE
  R0            15             295
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARMC3 MUTATED                                  0     0
  ARMC3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARMC3 MUTATED                           1    17
  ARMC3 WILD-TYPE                        28   360
D188V14, multiclass
                                  clus
vv                                 ARMC3 MUTATED ARMC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       17             360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V15, binary
                 cls
clus                0   1
  ARMC3 MUTATED     0  16
  ARMC3 WILD-TYPE   6 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC3 MUTATED      0   16
  ARMC3 WILD-TYPE    6  333
                        clus
vv                       ARMC3 MUTATED ARMC3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            16             333
[1] 2 2
[1] FALSE

Clustering(189) Variable = PIK3R4 MUTATION ANALYSIS
D189V1, survival
                  sevent
clus2                0   1
  PIK3R4 MUTATED    14   6
  PIK3R4 WILD-TYPE 301 135
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              20              436 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
               6              135 
$`PIK3R4 MUTATED`
TCGA-05-4396 TCGA-38-4631 TCGA-44-2657 TCGA-44-7667 TCGA-44-8117 TCGA-50-5930 
        9.96        11.64        13.15        36.07        12.66         9.27 
TCGA-50-5931 TCGA-50-6592 TCGA-55-7570 TCGA-55-7907 TCGA-55-8089 TCGA-64-1676 
       14.27        25.55         0.20         0.53         3.29        56.81 
TCGA-64-5781 TCGA-69-7765 TCGA-73-4666 TCGA-78-8640 TCGA-78-8662 TCGA-86-8671 
       51.25         5.42        26.30       214.62       110.50        27.58 
TCGA-93-A4JP TCGA-MN-A4N1 
       19.00        27.19 

$`PIK3R4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        46.98        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
       14.60        19.46        12.03         7.17        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        8.22        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         1.15         7.99         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 
       13.61        39.25        40.96        29.92        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       38.37        87.98         2.04        42.90        28.41        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        22.68        13.61         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
        1.15        13.91        30.84         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 
       16.44        19.00        14.30         3.81         0.20        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
             0.2              0.0 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
          214.62           223.96 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
          16.635           18.030 
[1] "0.2 - 214.6 (16.6)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.5"
D189V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PIK3R4 MUTATED         0        3        7         3         2          1
  PIK3R4 WILD-TYPE       4      120      126        43        65         69
                  vv
clus               STAGE IIIB STAGE IV
  PIK3R4 MUTATED            1        3
  PIK3R4 WILD-TYPE         10       22
D189V3, multiclass
            clus
vv           PIK3R4 MUTATED PIK3R4 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                7              126
  STAGE IIA               3               43
  STAGE IIB               2               65
  STAGE IIIA              1               69
  STAGE IIIB              1               10
  STAGE IV                3               22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3R4 MUTATED     5  11   1   2
  PIK3R4 WILD-TYPE 150 250  42  16
D189V4, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  T1              5              150
  T2             11              250
  T3              1               42
  T4              2               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"
                  vv
clus                N0  N1 N2+N3
  PIK3R4 MUTATED    12   5     1
  PIK3R4 WILD-TYPE 295  84    71
D189V5, multiclass
       clus
vv      PIK3R4 MUTATED PIK3R4 WILD-TYPE
  N0                12              295
  N1                 5               84
  N2+N3              1               71
[1] 3 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
  PIK3R4 MUTATED    14   2
  PIK3R4 WILD-TYPE 313  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     14    2
  PIK3R4 WILD-TYPE  313   21
   clus
vv  PIK3R4 MUTATED PIK3R4 WILD-TYPE
  0             14              313
  1              2               21
[1] 2 2
[1] FALSE
D189V7, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    10  10
  PIK3R4 WILD-TYPE 249 211
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     10   10
  PIK3R4 WILD-TYPE  249  211
        clus
vv       PIK3R4 MUTATED PIK3R4 WILD-TYPE
  FEMALE             10              249
  MALE               10              211
[1] 2 2
[1] FALSE
D189V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PIK3R4 MUTATED                            0                                 4
  PIK3R4 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PIK3R4 MUTATED                                                   14
  PIK3R4 WILD-TYPE                                                280
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PIK3R4 MUTATED                                            0
  PIK3R4 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PIK3R4 MUTATED                                               0
  PIK3R4 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  PIK3R4 MUTATED                                0
  PIK3R4 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  PIK3R4 MUTATED                                    0
  PIK3R4 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PIK3R4 MUTATED                              0                             2
  PIK3R4 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PIK3R4 MUTATED                                               0
  PIK3R4 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  PIK3R4 MUTATED                              0
  PIK3R4 WILD-TYPE                            9
D189V9, multiclass
                                                    clus
vv                                                   PIK3R4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             14
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   PIK3R4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V10, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED     2  18
  PIK3R4 WILD-TYPE  18 442
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED      2   18
  PIK3R4 WILD-TYPE   18  442
     clus
vv    PIK3R4 MUTATED PIK3R4 WILD-TYPE
  NO               2               18
  YES             18              442
[1] 2 2
[1] FALSE
D189V11, continuous
D189V12, continuous
                  vv
clus                R0  R1  R2  RX
  PIK3R4 MUTATED    14   0   0   1
  PIK3R4 WILD-TYPE 296  11   4  24
D189V13, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  R0             14              296
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R4 MUTATED                                  0     1
  PIK3R4 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R4 MUTATED                           3    13
  PIK3R4 WILD-TYPE                        26   364
D189V14, multiclass
                                  clus
vv                                 PIK3R4 MUTATED PIK3R4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                        13              364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V15, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED     0  17
  PIK3R4 WILD-TYPE   6 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED      0   17
  PIK3R4 WILD-TYPE    6  332
                        clus
vv                       PIK3R4 MUTATED PIK3R4 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             17              332
[1] 2 2
[1] FALSE

Clustering(190) Variable = ESRP1 MUTATION ANALYSIS
D190V1, survival
                 sevent
clus2               0   1
  ESRP1 MUTATED     7   1
  ESRP1 WILD-TYPE 308 140
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              8             448 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              1             140 
$`ESRP1 MUTATED`
TCGA-69-7980 TCGA-73-4676 TCGA-78-7155 TCGA-78-8640 TCGA-86-6851 TCGA-86-8054 
       12.56         5.39        38.50       214.62         5.88        24.49 
TCGA-95-7944 TCGA-MN-A4N4 
       12.39        38.63 

$`ESRP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30         2.93        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       29.98        26.30        15.35         4.31         1.32         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       18.67        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ESRP1 MUTATED ESRP1 WILD-TYPE 
           5.39            0.00 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
         214.62          223.96 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
         18.525          18.030 
[1] "5.4 - 214.6 (18.5)" "0.0 - 224.0 (18.0)"
[1] "hr=" "4.2"
D190V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ESRP1 MUTATED         1        2        1         3         1          0
  ESRP1 WILD-TYPE       3      121      132        43        66         70
                 vv
clus              STAGE IIIB STAGE IV
  ESRP1 MUTATED            0        0
  ESRP1 WILD-TYPE         11       25
D190V3, multiclass
            clus
vv           ESRP1 MUTATED ESRP1 WILD-TYPE
  STAGE I                1               3
  STAGE IA               2             121
  STAGE IB               1             132
  STAGE IIA              3              43
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of 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     5   3   0   0
  ESRP1 WILD-TYPE 150 258  43  18
D190V4, multiclass
    clus
vv   ESRP1 MUTATED ESRP1 WILD-TYPE
  T1             5             150
  T2             3             258
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ESRP1 MUTATED     4   4     0
  ESRP1 WILD-TYPE 303  85    72
D190V5, multiclass
       clus
vv      ESRP1 MUTATED ESRP1 WILD-TYPE
  N0                4             303
  N1                4              85
  N2+N3             0              72
[1] 3 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
  ESRP1 MUTATED     8   0
  ESRP1 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      8    0
  ESRP1 WILD-TYPE  319   23
   clus
vv  ESRP1 MUTATED ESRP1 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D190V7, binary
                 cls
clus                0   1
  ESRP1 MUTATED     2   6
  ESRP1 WILD-TYPE 257 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      2    6
  ESRP1 WILD-TYPE  257  215
        clus
vv       ESRP1 MUTATED ESRP1 WILD-TYPE
  FEMALE             2             257
  MALE               6             215
[1] 2 2
[1] FALSE
D190V8, continuous
[1] "Remove cluster labels:" "ESRP1 MUTATED"         
clus
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N5 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ESRP1 MUTATED                            1                                 1
  ESRP1 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ESRP1 MUTATED                                                    6
  ESRP1 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ESRP1 MUTATED                                            0
  ESRP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ESRP1 MUTATED                                               0
  ESRP1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ESRP1 MUTATED                                0
  ESRP1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ESRP1 MUTATED                                    0
  ESRP1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ESRP1 MUTATED                              0                             0
  ESRP1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ESRP1 MUTATED                                               0
  ESRP1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ESRP1 MUTATED                              0
  ESRP1 WILD-TYPE                            9
D190V9, multiclass
                                                    clus
vv                                                   ESRP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ESRP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V10, binary
                 cls
clus                0   1
  ESRP1 MUTATED     1   7
  ESRP1 WILD-TYPE  19 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      1    7
  ESRP1 WILD-TYPE   19  453
     clus
vv    ESRP1 MUTATED ESRP1 WILD-TYPE
  NO              1              19
  YES             7             453
[1] 2 2
[1] FALSE
D190V11, continuous
D190V12, continuous
                 vv
clus               R0  R1  R2  RX
  ESRP1 MUTATED     6   0   0   0
  ESRP1 WILD-TYPE 304  11   4  25
D190V13, multiclass
    clus
vv   ESRP1 MUTATED ESRP1 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESRP1 MUTATED                                  0     0
  ESRP1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESRP1 MUTATED                           0     7
  ESRP1 WILD-TYPE                        29   370
D190V14, multiclass
                                  clus
vv                                 ESRP1 MUTATED ESRP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V15, binary
                 cls
clus                0   1
  ESRP1 MUTATED     0   6
  ESRP1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      0    6
  ESRP1 WILD-TYPE    6  343
                        clus
vv                       ESRP1 MUTATED ESRP1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(191) Variable = GRN MUTATION ANALYSIS
D191V1, survival
               sevent
clus2             0   1
  GRN MUTATED     5   1
  GRN WILD-TYPE 310 140
  GRN MUTATED GRN WILD-TYPE 
            6           450 
  GRN MUTATED GRN WILD-TYPE 
            1           140 
$`GRN MUTATED`
TCGA-44-A479 TCGA-53-7624 TCGA-55-7727 TCGA-55-7907 TCGA-55-A491 TCGA-62-A472 
       15.98        34.29         1.12         0.53        20.58        29.92 

$`GRN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25         8.55        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.28         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       13.61        39.25        40.96        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  GRN MUTATED GRN WILD-TYPE 
         0.53          0.00 
  GRN MUTATED GRN WILD-TYPE 
        34.29        223.96 
  GRN MUTATED GRN WILD-TYPE 
        18.28         18.03 
[1] "0.5 - 34.3 (18.3)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.3"
D191V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GRN MUTATED         0        1        1         1         1          1
  GRN WILD-TYPE       4      122      132        45        66         69
               vv
clus            STAGE IIIB STAGE IV
  GRN MUTATED            0        1
  GRN WILD-TYPE         11       24
D191V3, multiclass
            clus
vv           GRN MUTATED GRN WILD-TYPE
  STAGE I              0             4
  STAGE IA             1           122
  STAGE IB             1           132
  STAGE IIA            1            45
  STAGE IIB            1            66
  STAGE IIIA           1            69
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  GRN MUTATED     2   3   1   0
  GRN WILD-TYPE 153 258  42  18
D191V4, multiclass
    clus
vv   GRN MUTATED GRN WILD-TYPE
  T1           2           153
  T2           3           258
  T3           1            42
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  GRN MUTATED     4   1     1
  GRN WILD-TYPE 303  88    71
D191V5, multiclass
       clus
vv      GRN MUTATED GRN WILD-TYPE
  N0              4           303
  N1              1            88
  N2+N3           1            71
[1] 3 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
  GRN MUTATED     1   1
  GRN WILD-TYPE 326  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  GRN MUTATED      1    1
  GRN WILD-TYPE  326   22
   clus
vv  GRN MUTATED GRN WILD-TYPE
  0           1           326
  1           1            22
[1] 2 2
[1] FALSE
D191V7, binary
               cls
clus              0   1
  GRN MUTATED     3   3
  GRN WILD-TYPE 256 218
[1] "tbl2"
               cls
clus            [,1] [,2]
  GRN MUTATED      3    3
  GRN WILD-TYPE  256  218
        clus
vv       GRN MUTATED GRN WILD-TYPE
  FEMALE           3           256
  MALE             3           218
[1] 2 2
[1] FALSE
D191V8, continuous
[1] "Remove cluster labels:" "GRN MUTATED"           
clus
  GRN MUTATED GRN WILD-TYPE 
            1            83 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-62-A470    TCGA-62-A471    TCGA-64-1677    TCGA-64-1681    TCGA-64-5778 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520    TCGA-73-4659 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-86-8279    TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-86-8669    TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
   TCGA-MN-A4N1    TCGA-MN-A4N4    TCGA-MN-A4N5 
"GRN WILD-TYPE" "GRN WILD-TYPE" "GRN WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GRN MUTATED                            0                                 0
  GRN WILD-TYPE                         18                               102
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GRN MUTATED                                                    6
  GRN WILD-TYPE                                                288
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GRN MUTATED                                            0
  GRN WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GRN MUTATED                                               0
  GRN WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  GRN MUTATED                                0
  GRN WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  GRN MUTATED                                    0                            0
  GRN WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  GRN MUTATED                               0
  GRN WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GRN MUTATED                                               0
  GRN WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  GRN MUTATED                              0
  GRN WILD-TYPE                            9
D191V9, multiclass
                                                    clus
vv                                                   GRN MUTATED GRN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            0           102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           6           288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V10, binary
               cls
clus              0   1
  GRN MUTATED     0   6
  GRN WILD-TYPE  20 454
[1] "tbl2"
               cls
clus            [,1] [,2]
  GRN MUTATED      0    6
  GRN WILD-TYPE   20  454
     clus
vv    GRN MUTATED GRN WILD-TYPE
  NO            0            20
  YES           6           454
[1] 2 2
[1] FALSE
D191V11, continuous
D191V12, continuous
               vv
clus             R0  R1  R2  RX
  GRN MUTATED     6   0   0   0
  GRN WILD-TYPE 304  11   4  25
D191V13, multiclass
    clus
vv   GRN MUTATED GRN WILD-TYPE
  R0           6           304
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRN MUTATED                                  0     0
  GRN WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GRN MUTATED                           1     5
  GRN WILD-TYPE                        28   372
D191V14, multiclass
                                  clus
vv                                 GRN MUTATED GRN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                      5           372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V15, binary
               cls
clus              0   1
  GRN MUTATED     1   5
  GRN WILD-TYPE   5 344
[1] "tbl2"
               cls
clus            [,1] [,2]
  GRN MUTATED      1    5
  GRN WILD-TYPE    5  344
                        clus
vv                       GRN MUTATED GRN WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO           5           344
[1] 2 2
[1] FALSE

Clustering(192) Variable = CYTH4 MUTATION ANALYSIS
D192V1, survival
                 sevent
clus2               0   1
  CYTH4 MUTATED     5   0
  CYTH4 WILD-TYPE 310 141
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              5             451 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              0             141 
$`CYTH4 MUTATED`
TCGA-55-7995 TCGA-55-A492 TCGA-78-7153 TCGA-93-7348 TCGA-99-8028 
        0.16        19.59        24.99         4.18        36.76 

$`CYTH4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
       22.65        20.71        21.40         1.58        20.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
       20.58        35.93        21.90        39.52        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CYTH4 MUTATED CYTH4 WILD-TYPE 
           0.16            0.00 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
          36.76          223.96 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
          19.59           17.98 
[1] "0.2 - 36.8 (19.6)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "3300000"
D192V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CYTH4 MUTATED         0        4        1         0         0          0
  CYTH4 WILD-TYPE       4      119      132        46        67         70
                 vv
clus              STAGE IIIB STAGE IV
  CYTH4 MUTATED            0        0
  CYTH4 WILD-TYPE         11       25
D192V3, multiclass
            clus
vv           CYTH4 MUTATED CYTH4 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               1             132
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CYTH4 MUTATED     4   1   0   0
  CYTH4 WILD-TYPE 151 260  43  18
D192V4, multiclass
    clus
vv   CYTH4 MUTATED CYTH4 WILD-TYPE
  T1             4             151
  T2             1             260
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  CYTH4 MUTATED     5   0     0
  CYTH4 WILD-TYPE 302  89    72
D192V5, multiclass
       clus
vv      CYTH4 MUTATED CYTH4 WILD-TYPE
  N0                5             302
  N1                0              89
  N2+N3             0              72
[1] 3 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
  CYTH4 MUTATED     3   0
  CYTH4 WILD-TYPE 324  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      3    0
  CYTH4 WILD-TYPE  324   23
   clus
vv  CYTH4 MUTATED CYTH4 WILD-TYPE
  0             3             324
  1             0              23
[1] 2 2
[1] FALSE
D192V7, binary
                 cls
clus                0   1
  CYTH4 MUTATED     5   0
  CYTH4 WILD-TYPE 254 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      5    0
  CYTH4 WILD-TYPE  254  221
        clus
vv       CYTH4 MUTATED CYTH4 WILD-TYPE
  FEMALE             5             254
  MALE               0             221
[1] 2 2
[1] FALSE
D192V8, continuous
[1] "Remove cluster labels:" "CYTH4 MUTATED"         
clus
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CYTH4 MUTATED                            0                                 1
  CYTH4 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CYTH4 MUTATED                                                    4
  CYTH4 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CYTH4 MUTATED                                            0
  CYTH4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CYTH4 MUTATED                                               0
  CYTH4 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CYTH4 MUTATED                                0
  CYTH4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CYTH4 MUTATED                                    0
  CYTH4 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CYTH4 MUTATED                              0                             0
  CYTH4 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CYTH4 MUTATED                                               0
  CYTH4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CYTH4 MUTATED                              0
  CYTH4 WILD-TYPE                            9
D192V9, multiclass
                                                    clus
vv                                                   CYTH4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CYTH4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V10, binary
                 cls
clus                0   1
  CYTH4 MUTATED     0   5
  CYTH4 WILD-TYPE  20 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      0    5
  CYTH4 WILD-TYPE   20  455
     clus
vv    CYTH4 MUTATED CYTH4 WILD-TYPE
  NO              0              20
  YES             5             455
[1] 2 2
[1] FALSE
D192V11, continuous
D192V12, continuous
                 vv
clus               R0  R1  R2  RX
  CYTH4 MUTATED     5   0   0   0
  CYTH4 WILD-TYPE 305  11   4  25
D192V13, multiclass
    clus
vv   CYTH4 MUTATED CYTH4 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYTH4 MUTATED                                  0     0
  CYTH4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CYTH4 MUTATED                           1     4
  CYTH4 WILD-TYPE                        28   373
D192V14, multiclass
                                  clus
vv                                 CYTH4 MUTATED CYTH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V15, binary
                 cls
clus                0   1
  CYTH4 MUTATED     0   4
  CYTH4 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      0    4
  CYTH4 WILD-TYPE    6  345
                        clus
vv                       CYTH4 MUTATED CYTH4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(193) Variable = SEC23IP MUTATION ANALYSIS
D193V1, survival
                   sevent
clus2                 0   1
  SEC23IP MUTATED     8   1
  SEC23IP WILD-TYPE 307 140
  SEC23IP MUTATED SEC23IP WILD-TYPE 
                9               447 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
                1               140 
$`SEC23IP MUTATED`
TCGA-35-4123 TCGA-44-A47F TCGA-49-6743 TCGA-50-5930 TCGA-55-7907 TCGA-55-8507 
        5.98        11.08        12.13         9.27         0.53         0.26 
TCGA-55-A4DG TCGA-86-8074 TCGA-91-6848 
       19.99         0.79         7.36 

$`SEC23IP WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        14.63        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.36         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        15.81        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57        24.33        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23        27.68         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SEC23IP MUTATED SEC23IP WILD-TYPE 
             0.26              0.00 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
            19.99            223.96 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
             7.36             18.64 
[1] "0.3 - 20.0 (7.4)"   "0.0 - 224.0 (18.6)"
[1] "hr=" "1.4"
D193V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SEC23IP MUTATED         0        3        0         2         1          3
  SEC23IP WILD-TYPE       4      120      133        44        66         67
                   vv
clus                STAGE IIIB STAGE IV
  SEC23IP MUTATED            0        0
  SEC23IP WILD-TYPE         11       25
D193V3, multiclass
            clus
vv           SEC23IP MUTATED SEC23IP WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 3               120
  STAGE IB                 0               133
  STAGE IIA                2                44
  STAGE IIB                1                66
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SEC23IP MUTATED     5   4   0   0
  SEC23IP WILD-TYPE 150 257  43  18
D193V4, multiclass
    clus
vv   SEC23IP MUTATED SEC23IP WILD-TYPE
  T1               5               150
  T2               4               257
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  SEC23IP MUTATED     3   3     3
  SEC23IP WILD-TYPE 304  86    69
D193V5, multiclass
       clus
vv      SEC23IP MUTATED SEC23IP WILD-TYPE
  N0                  3               304
  N1                  3                86
  N2+N3               3                69
[1] 3 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
  SEC23IP MUTATED     4   0
  SEC23IP WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED      4    0
  SEC23IP WILD-TYPE  323   23
   clus
vv  SEC23IP MUTATED SEC23IP WILD-TYPE
  0               4               323
  1               0                23
[1] 2 2
[1] FALSE
D193V7, binary
                   cls
clus                  0   1
  SEC23IP MUTATED     2   7
  SEC23IP WILD-TYPE 257 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED      2    7
  SEC23IP WILD-TYPE  257  214
        clus
vv       SEC23IP MUTATED SEC23IP WILD-TYPE
  FEMALE               2               257
  MALE                 7               214
[1] 2 2
[1] FALSE
D193V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SEC23IP MUTATED                            0
  SEC23IP WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SEC23IP MUTATED                                   1
  SEC23IP WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SEC23IP MUTATED                                                    7
  SEC23IP WILD-TYPE                                                287
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SEC23IP MUTATED                                            0
  SEC23IP WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SEC23IP MUTATED                                               0
  SEC23IP WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SEC23IP MUTATED                                1
  SEC23IP WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SEC23IP MUTATED                                    0
  SEC23IP WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SEC23IP MUTATED                              0                             0
  SEC23IP WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SEC23IP MUTATED                                               0
  SEC23IP WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SEC23IP MUTATED                              0
  SEC23IP WILD-TYPE                            9
D193V9, multiclass
                                                    clus
vv                                                   SEC23IP MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SEC23IP WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V10, binary
                   cls
clus                  0   1
  SEC23IP MUTATED     1   8
  SEC23IP WILD-TYPE  19 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED      1    8
  SEC23IP WILD-TYPE   19  452
     clus
vv    SEC23IP MUTATED SEC23IP WILD-TYPE
  NO                1                19
  YES               8               452
[1] 2 2
[1] FALSE
D193V11, continuous
D193V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SEC23IP MUTATED     5   0   0   0
  SEC23IP WILD-TYPE 305  11   4  25
D193V13, multiclass
    clus
vv   SEC23IP MUTATED SEC23IP WILD-TYPE
  R0               5               305
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC23IP MUTATED                                  0     0
  SEC23IP WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SEC23IP MUTATED                           0     9
  SEC23IP WILD-TYPE                        29   368
D193V14, multiclass
                                  clus
vv                                 SEC23IP MUTATED SEC23IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          9               368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V15, binary
                   cls
clus                  0   1
  SEC23IP MUTATED     0   8
  SEC23IP WILD-TYPE   6 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED      0    8
  SEC23IP WILD-TYPE    6  341
                        clus
vv                       SEC23IP MUTATED SEC23IP WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               8               341
[1] 2 2
[1] FALSE

Clustering(194) Variable = LARP4 MUTATION ANALYSIS
D194V1, survival
                 sevent
clus2               0   1
  LARP4 MUTATED     5   4
  LARP4 WILD-TYPE 310 137
  LARP4 MUTATED LARP4 WILD-TYPE 
              9             447 
  LARP4 MUTATED LARP4 WILD-TYPE 
              4             137 
$`LARP4 MUTATED`
TCGA-05-4389 TCGA-05-4417 TCGA-50-5933 TCGA-62-A46O TCGA-73-4668 TCGA-78-7155 
       45.01        14.96        78.67        47.80        15.35        38.50 
TCGA-86-8278 TCGA-MP-A4TF TCGA-NJ-A4YP 
       15.65        11.05         1.64 

$`LARP4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        0.10        52.60        23.38        29.98        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        2.43        10.09        29.46        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  LARP4 MUTATED LARP4 WILD-TYPE 
           1.64            0.00 
  LARP4 MUTATED LARP4 WILD-TYPE 
          78.67          223.96 
  LARP4 MUTATED LARP4 WILD-TYPE 
          15.65           18.08 
[1] "1.6 - 78.7 (15.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D194V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LARP4 MUTATED         0        1        4         1         2          0
  LARP4 WILD-TYPE       4      122      129        45        65         70
                 vv
clus              STAGE IIIB STAGE IV
  LARP4 MUTATED            1        0
  LARP4 WILD-TYPE         10       25
D194V3, multiclass
            clus
vv           LARP4 MUTATED LARP4 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LARP4 MUTATED     1   7   0   1
  LARP4 WILD-TYPE 154 254  43  17
D194V4, multiclass
    clus
vv   LARP4 MUTATED LARP4 WILD-TYPE
  T1             1             154
  T2             7             254
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  LARP4 MUTATED     6   2     1
  LARP4 WILD-TYPE 301  87    71
D194V5, multiclass
       clus
vv      LARP4 MUTATED LARP4 WILD-TYPE
  N0                6             301
  N1                2              87
  N2+N3             1              71
[1] 3 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
  LARP4 MUTATED     9   0
  LARP4 WILD-TYPE 318  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP4 MUTATED      9    0
  LARP4 WILD-TYPE  318   23
   clus
vv  LARP4 MUTATED LARP4 WILD-TYPE
  0             9             318
  1             0              23
[1] 2 2
[1] FALSE
D194V7, binary
                 cls
clus                0   1
  LARP4 MUTATED     5   4
  LARP4 WILD-TYPE 254 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP4 MUTATED      5    4
  LARP4 WILD-TYPE  254  217
        clus
vv       LARP4 MUTATED LARP4 WILD-TYPE
  FEMALE             5             254
  MALE               4             217
[1] 2 2
[1] FALSE
D194V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LARP4 MUTATED                            0                                 2
  LARP4 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LARP4 MUTATED                                                    5
  LARP4 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LARP4 MUTATED                                            0
  LARP4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LARP4 MUTATED                                               0
  LARP4 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  LARP4 MUTATED                                0
  LARP4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  LARP4 MUTATED                                    1
  LARP4 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LARP4 MUTATED                              0                             1
  LARP4 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LARP4 MUTATED                                               0
  LARP4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  LARP4 MUTATED                              0
  LARP4 WILD-TYPE                            9
D194V9, multiclass
                                                    clus
vv                                                   LARP4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   LARP4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V10, binary
                 cls
clus                0   1
  LARP4 MUTATED     1   8
  LARP4 WILD-TYPE  19 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP4 MUTATED      1    8
  LARP4 WILD-TYPE   19  452
     clus
vv    LARP4 MUTATED LARP4 WILD-TYPE
  NO              1              19
  YES             8             452
[1] 2 2
[1] FALSE
D194V11, continuous
D194V12, continuous
                 vv
clus               R0  R1  R2  RX
  LARP4 MUTATED     7   0   0   0
  LARP4 WILD-TYPE 303  11   4  25
D194V13, multiclass
    clus
vv   LARP4 MUTATED LARP4 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LARP4 MUTATED                                  1     0
  LARP4 WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LARP4 MUTATED                           0     6
  LARP4 WILD-TYPE                        29   371
D194V14, multiclass
                                  clus
vv                                 LARP4 MUTATED LARP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V15, binary
                 cls
clus                0   1
  LARP4 MUTATED     0   6
  LARP4 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP4 MUTATED      0    6
  LARP4 WILD-TYPE    6  343
                        clus
vv                       LARP4 MUTATED LARP4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(195) Variable = SLAMF8 MUTATION ANALYSIS
D195V1, survival
                  sevent
clus2                0   1
  SLAMF8 MUTATED     4   5
  SLAMF8 WILD-TYPE 311 136
  SLAMF8 MUTATED SLAMF8 WILD-TYPE 
               9              447 
  SLAMF8 MUTATED SLAMF8 WILD-TYPE 
               5              136 
$`SLAMF8 MUTATED`
TCGA-38-4632 TCGA-44-3918 TCGA-78-8660 TCGA-78-8662 TCGA-86-8672 TCGA-91-6836 
       44.61        34.06        10.55       110.50         0.62        13.71 
TCGA-95-7947 TCGA-95-A4VN TCGA-MP-A4T7 
       15.68        18.18         5.49 

$`SLAMF8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
      214.62        39.75        77.59        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       14.60         1.15        13.91        30.84        27.58        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       18.67        12.39        15.65        27.29         2.76        21.40 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SLAMF8 MUTATED SLAMF8 WILD-TYPE 
            0.62             0.00 
  SLAMF8 MUTATED SLAMF8 WILD-TYPE 
          110.50           223.96 
  SLAMF8 MUTATED SLAMF8 WILD-TYPE 
           15.68            18.08 
[1] "0.6 - 110.5 (15.7)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D195V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLAMF8 MUTATED         0        2        2         1         2          0
  SLAMF8 WILD-TYPE       4      121      131        45        65         70
                  vv
clus               STAGE IIIB STAGE IV
  SLAMF8 MUTATED            0        2
  SLAMF8 WILD-TYPE         11       23
D195V3, multiclass
            clus
vv           SLAMF8 MUTATED SLAMF8 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                2              131
  STAGE IIA               1               45
  STAGE IIB               2               65
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLAMF8 MUTATED     2   6   1   0
  SLAMF8 WILD-TYPE 153 255  42  18
D195V4, multiclass
    clus
vv   SLAMF8 MUTATED SLAMF8 WILD-TYPE
  T1              2              153
  T2              6              255
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  SLAMF8 MUTATED     6   3     0
  SLAMF8 WILD-TYPE 301  86    72
D195V5, multiclass
       clus
vv      SLAMF8 MUTATED SLAMF8 WILD-TYPE
  N0                 6              301
  N1                 3               86
  N2+N3              0               72
[1] 3 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
  SLAMF8 MUTATED     6   2
  SLAMF8 WILD-TYPE 321  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF8 MUTATED      6    2
  SLAMF8 WILD-TYPE  321   21
   clus
vv  SLAMF8 MUTATED SLAMF8 WILD-TYPE
  0              6              321
  1              2               21
[1] 2 2
[1] FALSE
D195V7, binary
                  cls
clus                 0   1
  SLAMF8 MUTATED     5   4
  SLAMF8 WILD-TYPE 254 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF8 MUTATED      5    4
  SLAMF8 WILD-TYPE  254  217
        clus
vv       SLAMF8 MUTATED SLAMF8 WILD-TYPE
  FEMALE              5              254
  MALE                4              217
[1] 2 2
[1] FALSE
D195V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLAMF8 MUTATED                            0                                 1
  SLAMF8 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLAMF8 MUTATED                                                    7
  SLAMF8 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLAMF8 MUTATED                                            0
  SLAMF8 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLAMF8 MUTATED                                               0
  SLAMF8 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SLAMF8 MUTATED                                0
  SLAMF8 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SLAMF8 MUTATED                                    0
  SLAMF8 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLAMF8 MUTATED                              0                             0
  SLAMF8 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLAMF8 MUTATED                                               1
  SLAMF8 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SLAMF8 MUTATED                              0
  SLAMF8 WILD-TYPE                            9
D195V9, multiclass
                                                    clus
vv                                                   SLAMF8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SLAMF8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V10, binary
                  cls
clus                 0   1
  SLAMF8 MUTATED     0   9
  SLAMF8 WILD-TYPE  20 451
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF8 MUTATED      0    9
  SLAMF8 WILD-TYPE   20  451
     clus
vv    SLAMF8 MUTATED SLAMF8 WILD-TYPE
  NO               0               20
  YES              9              451
[1] 2 2
[1] FALSE
D195V11, continuous
D195V12, continuous
                  vv
clus                R0  R1  R2  RX
  SLAMF8 MUTATED     8   0   0   0
  SLAMF8 WILD-TYPE 302  11   4  25
D195V13, multiclass
    clus
vv   SLAMF8 MUTATED SLAMF8 WILD-TYPE
  R0              8              302
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLAMF8 MUTATED                                  0     0
  SLAMF8 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLAMF8 MUTATED                           1     5
  SLAMF8 WILD-TYPE                        28   372
D195V14, multiclass
                                  clus
vv                                 SLAMF8 MUTATED SLAMF8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V15, binary
                  cls
clus                 0   1
  SLAMF8 MUTATED     0   6
  SLAMF8 WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF8 MUTATED      0    6
  SLAMF8 WILD-TYPE    6  343
                        clus
vv                       SLAMF8 MUTATED SLAMF8 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              343
[1] 2 2
[1] FALSE

Clustering(196) Variable = IGDCC4 MUTATION ANALYSIS
D196V1, survival
                  sevent
clus2                0   1
  IGDCC4 MUTATED    16   7
  IGDCC4 WILD-TYPE 299 134
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
              23              433 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
               7              134 
$`IGDCC4 MUTATED`
TCGA-05-4382 TCGA-05-4398 TCGA-05-4424 TCGA-05-5425 TCGA-35-4122 TCGA-38-4631 
       19.96        47.05        30.02        29.00         7.40        11.64 
TCGA-44-5644 TCGA-49-4486 TCGA-50-5049 TCGA-50-5930 TCGA-55-7907 TCGA-55-8506 
       28.37        76.21        70.55         9.27         0.53         0.36 
TCGA-55-A490 TCGA-62-A46O TCGA-62-A46Y TCGA-64-5781 TCGA-67-3771 TCGA-69-7980 
        1.58        47.80        13.61        51.25        20.05        12.56 
TCGA-73-4658 TCGA-73-4677 TCGA-86-8076 TCGA-91-8499 TCGA-97-A4M0 
       52.60         1.25        16.08         1.18        21.44 

$`IGDCC4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        29.98        12.00        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 
        4.96        22.03         9.04         2.04         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        72.30        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       42.90        28.41        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.42         7.56         6.05         2.30         2.93        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24         7.04         2.01         0.10        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        15.75        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
            0.36             0.00 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
           76.21           223.96 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
           19.96            17.98 
[1] "0.4 - 76.2 (20.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D196V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IGDCC4 MUTATED         1        7        8         2         3          2
  IGDCC4 WILD-TYPE       3      116      125        44        64         68
                  vv
clus               STAGE IIIB STAGE IV
  IGDCC4 MUTATED            1        0
  IGDCC4 WILD-TYPE         10       25
D196V3, multiclass
            clus
vv           IGDCC4 MUTATED IGDCC4 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                7              116
  STAGE IB                8              125
  STAGE IIA               2               44
  STAGE IIB               3               64
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     6  15   2   1
  IGDCC4 WILD-TYPE 149 246  41  17
D196V4, multiclass
    clus
vv   IGDCC4 MUTATED IGDCC4 WILD-TYPE
  T1              6              149
  T2             15              246
  T3              2               41
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  IGDCC4 MUTATED    19   2     3
  IGDCC4 WILD-TYPE 288  87    69
D196V5, multiclass
       clus
vv      IGDCC4 MUTATED IGDCC4 WILD-TYPE
  N0                19              288
  N1                 2               87
  N2+N3              3               69
[1] 3 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
  IGDCC4 MUTATED    19   0
  IGDCC4 WILD-TYPE 308  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED     19    0
  IGDCC4 WILD-TYPE  308   23
   clus
vv  IGDCC4 MUTATED IGDCC4 WILD-TYPE
  0             19              308
  1              0               23
[1] 2 2
[1] FALSE
D196V7, binary
                  cls
clus                 0   1
  IGDCC4 MUTATED    12  12
  IGDCC4 WILD-TYPE 247 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED     12   12
  IGDCC4 WILD-TYPE  247  209
        clus
vv       IGDCC4 MUTATED IGDCC4 WILD-TYPE
  FEMALE             12              247
  MALE               12              209
[1] 2 2
[1] FALSE
D196V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  IGDCC4 MUTATED                            0                                 8
  IGDCC4 WILD-TYPE                         18                                94
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IGDCC4 MUTATED                                                   15
  IGDCC4 WILD-TYPE                                                279
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IGDCC4 MUTATED                                            0
  IGDCC4 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IGDCC4 MUTATED                                               0
  IGDCC4 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  IGDCC4 MUTATED                                0
  IGDCC4 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  IGDCC4 MUTATED                                    0
  IGDCC4 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  IGDCC4 MUTATED                              0                             1
  IGDCC4 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IGDCC4 MUTATED                                               0
  IGDCC4 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  IGDCC4 MUTATED                              0
  IGDCC4 WILD-TYPE                            9
D196V9, multiclass
                                                    clus
vv                                                   IGDCC4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   IGDCC4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V10, binary
                  cls
clus                 0   1
  IGDCC4 MUTATED     2  22
  IGDCC4 WILD-TYPE  18 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED      2   22
  IGDCC4 WILD-TYPE   18  438
     clus
vv    IGDCC4 MUTATED IGDCC4 WILD-TYPE
  NO               2               18
  YES             22              438
[1] 2 2
[1] FALSE
D196V11, continuous
D196V12, continuous
                  vv
clus                R0  R1  R2  RX
  IGDCC4 MUTATED    17   1   0   0
  IGDCC4 WILD-TYPE 293  10   4  25
D196V13, multiclass
    clus
vv   IGDCC4 MUTATED IGDCC4 WILD-TYPE
  R0             17              293
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGDCC4 MUTATED                                  0     0
  IGDCC4 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IGDCC4 MUTATED                           1    18
  IGDCC4 WILD-TYPE                        28   359
D196V14, multiclass
                                  clus
vv                                 IGDCC4 MUTATED IGDCC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        18              359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V15, binary
                  cls
clus                 0   1
  IGDCC4 MUTATED     0  19
  IGDCC4 WILD-TYPE   6 330
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED      0   19
  IGDCC4 WILD-TYPE    6  330
                        clus
vv                       IGDCC4 MUTATED IGDCC4 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             19              330
[1] 2 2
[1] FALSE

Clustering(197) Variable = NPBWR2 MUTATION ANALYSIS
D197V1, survival
                  sevent
clus2                0   1
  NPBWR2 MUTATED     6   2
  NPBWR2 WILD-TYPE 309 139
  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
               8              448 
  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
               2              139 
$`NPBWR2 MUTATED`
TCGA-55-8506 TCGA-55-8620 TCGA-64-5781 TCGA-69-7979 TCGA-78-7220 TCGA-86-8358 
        0.36         2.17        51.25         2.93        26.53        21.47 
TCGA-93-A4JQ TCGA-MP-A4T2 
       17.29        37.35 

$`NPBWR2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.58         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       16.08        15.65        15.85        23.05        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 
       38.63         2.76        86.14        58.45        49.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
            0.36             0.00 
  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
           51.25           223.96 
  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
           19.38            18.03 
[1] "0.4 - 51.2 (19.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D197V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NPBWR2 MUTATED         0        2        3         0         1          1
  NPBWR2 WILD-TYPE       4      121      130        46        66         69
                  vv
clus               STAGE IIIB STAGE IV
  NPBWR2 MUTATED            0        1
  NPBWR2 WILD-TYPE         11       24
D197V3, multiclass
            clus
vv           NPBWR2 MUTATED NPBWR2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                3              130
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NPBWR2 MUTATED     3   4   1   0
  NPBWR2 WILD-TYPE 152 257  42  18
D197V4, multiclass
    clus
vv   NPBWR2 MUTATED NPBWR2 WILD-TYPE
  T1              3              152
  T2              4              257
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  NPBWR2 MUTATED     6   1     1
  NPBWR2 WILD-TYPE 301  88    71
D197V5, multiclass
       clus
vv      NPBWR2 MUTATED NPBWR2 WILD-TYPE
  N0                 6              301
  N1                 1               88
  N2+N3              1               71
[1] 3 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
  NPBWR2 MUTATED     4   1
  NPBWR2 WILD-TYPE 323  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NPBWR2 MUTATED      4    1
  NPBWR2 WILD-TYPE  323   22
   clus
vv  NPBWR2 MUTATED NPBWR2 WILD-TYPE
  0              4              323
  1              1               22
[1] 2 2
[1] FALSE
D197V7, binary
                  cls
clus                 0   1
  NPBWR2 MUTATED     4   4
  NPBWR2 WILD-TYPE 255 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NPBWR2 MUTATED      4    4
  NPBWR2 WILD-TYPE  255  217
        clus
vv       NPBWR2 MUTATED NPBWR2 WILD-TYPE
  FEMALE              4              255
  MALE                4              217
[1] 2 2
[1] FALSE
D197V8, continuous
[1] "Remove cluster labels:" "NPBWR2 MUTATED"        
clus
  NPBWR2 MUTATED NPBWR2 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-A48Z       TCGA-55-A490 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8359 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"NPBWR2 WILD-TYPE" "NPBWR2 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NPBWR2 MUTATED                            2                                 2
  NPBWR2 WILD-TYPE                         16                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NPBWR2 MUTATED                                                    4
  NPBWR2 WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NPBWR2 MUTATED                                            0
  NPBWR2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NPBWR2 MUTATED                                               0
  NPBWR2 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  NPBWR2 MUTATED                                0
  NPBWR2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  NPBWR2 MUTATED                                    0
  NPBWR2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NPBWR2 MUTATED                              0                             0
  NPBWR2 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NPBWR2 MUTATED                                               0
  NPBWR2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  NPBWR2 MUTATED                              0
  NPBWR2 WILD-TYPE                            9
D197V9, multiclass
                                                    clus
vv                                                   NPBWR2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   NPBWR2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V10, binary
                  cls
clus                 0   1
  NPBWR2 MUTATED     1   7
  NPBWR2 WILD-TYPE  19 453
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NPBWR2 MUTATED      1    7
  NPBWR2 WILD-TYPE   19  453
     clus
vv    NPBWR2 MUTATED NPBWR2 WILD-TYPE
  NO               1               19
  YES              7              453
[1] 2 2
[1] FALSE
D197V11, continuous
D197V12, continuous
                  vv
clus                R0  R1  R2  RX
  NPBWR2 MUTATED     6   0   0   1
  NPBWR2 WILD-TYPE 304  11   4  24
D197V13, multiclass
    clus
vv   NPBWR2 MUTATED NPBWR2 WILD-TYPE
  R0              6              304
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NPBWR2 MUTATED                                  0     0
  NPBWR2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NPBWR2 MUTATED                           0     8
  NPBWR2 WILD-TYPE                        29   369
D197V14, multiclass
                                  clus
vv                                 NPBWR2 MUTATED NPBWR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         8              369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V15, binary
                  cls
clus                 0   1
  NPBWR2 MUTATED     0   7
  NPBWR2 WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NPBWR2 MUTATED      0    7
  NPBWR2 WILD-TYPE    6  342
                        clus
vv                       NPBWR2 MUTATED NPBWR2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(198) Variable = FLRT3 MUTATION ANALYSIS
D198V1, survival
                 sevent
clus2               0   1
  FLRT3 MUTATED     7   1
  FLRT3 WILD-TYPE 308 140
  FLRT3 MUTATED FLRT3 WILD-TYPE 
              8             448 
  FLRT3 MUTATED FLRT3 WILD-TYPE 
              1             140 
$`FLRT3 MUTATED`
TCGA-55-7574 TCGA-55-8508 TCGA-69-7765 TCGA-78-7155 TCGA-78-8640 TCGA-91-6836 
        3.12         0.49         5.42        38.50       214.62        13.71 
TCGA-93-8067 TCGA-99-7458 
        6.12        24.56 

$`FLRT3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        10.55        32.68        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  FLRT3 MUTATED FLRT3 WILD-TYPE 
           0.49            0.00 
  FLRT3 MUTATED FLRT3 WILD-TYPE 
         214.62          223.96 
  FLRT3 MUTATED FLRT3 WILD-TYPE 
          9.915          18.100 
[1] "0.5 - 214.6 (9.9)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "3.5"
D198V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FLRT3 MUTATED         0        0        4         2         0          1
  FLRT3 WILD-TYPE       4      123      129        44        67         69
                 vv
clus              STAGE IIIB STAGE IV
  FLRT3 MUTATED            0        1
  FLRT3 WILD-TYPE         11       24
D198V3, multiclass
            clus
vv           FLRT3 MUTATED FLRT3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               4             129
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FLRT3 MUTATED     1   5   0   2
  FLRT3 WILD-TYPE 154 256  43  16
D198V4, multiclass
    clus
vv   FLRT3 MUTATED FLRT3 WILD-TYPE
  T1             1             154
  T2             5             256
  T3             0              43
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  FLRT3 MUTATED     6   2     0
  FLRT3 WILD-TYPE 301  87    72
D198V5, multiclass
       clus
vv      FLRT3 MUTATED FLRT3 WILD-TYPE
  N0                6             301
  N1                2              87
  N2+N3             0              72
[1] 3 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
  FLRT3 MUTATED     4   0
  FLRT3 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FLRT3 MUTATED      4    0
  FLRT3 WILD-TYPE  323   23
   clus
vv  FLRT3 MUTATED FLRT3 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D198V7, binary
                 cls
clus                0   1
  FLRT3 MUTATED     4   4
  FLRT3 WILD-TYPE 255 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FLRT3 MUTATED      4    4
  FLRT3 WILD-TYPE  255  217
        clus
vv       FLRT3 MUTATED FLRT3 WILD-TYPE
  FEMALE             4             255
  MALE               4             217
[1] 2 2
[1] FALSE
D198V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FLRT3 MUTATED                            0                                 1
  FLRT3 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FLRT3 MUTATED                                                    5
  FLRT3 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FLRT3 MUTATED                                            0
  FLRT3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FLRT3 MUTATED                                               1
  FLRT3 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FLRT3 MUTATED                                0
  FLRT3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FLRT3 MUTATED                                    0
  FLRT3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FLRT3 MUTATED                              0                             0
  FLRT3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FLRT3 MUTATED                                               0
  FLRT3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FLRT3 MUTATED                              1
  FLRT3 WILD-TYPE                            8
D198V9, multiclass
                                                    clus
vv                                                   FLRT3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   FLRT3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V10, binary
                 cls
clus                0   1
  FLRT3 MUTATED     1   7
  FLRT3 WILD-TYPE  19 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FLRT3 MUTATED      1    7
  FLRT3 WILD-TYPE   19  453
     clus
vv    FLRT3 MUTATED FLRT3 WILD-TYPE
  NO              1              19
  YES             7             453
[1] 2 2
[1] FALSE
D198V11, continuous
D198V12, continuous
                 vv
clus               R0  R1  R2  RX
  FLRT3 MUTATED     4   1   0   1
  FLRT3 WILD-TYPE 306  10   4  24
D198V13, multiclass
    clus
vv   FLRT3 MUTATED FLRT3 WILD-TYPE
  R0             4             306
  R1             1              10
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLRT3 MUTATED                                  0     1
  FLRT3 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FLRT3 MUTATED                           2     4
  FLRT3 WILD-TYPE                        27   373
D198V14, multiclass
                                  clus
vv                                 FLRT3 MUTATED FLRT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V15, binary
                 cls
clus                0   1
  FLRT3 MUTATED     0   6
  FLRT3 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FLRT3 MUTATED      0    6
  FLRT3 WILD-TYPE    6  343
                        clus
vv                       FLRT3 MUTATED FLRT3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(199) Variable = MYO1G MUTATION ANALYSIS
D199V1, survival
                 sevent
clus2               0   1
  MYO1G MUTATED    10   2
  MYO1G WILD-TYPE 305 139
  MYO1G MUTATED MYO1G WILD-TYPE 
             12             444 
  MYO1G MUTATED MYO1G WILD-TYPE 
              2             139 
$`MYO1G MUTATED`
TCGA-35-4123 TCGA-44-2656 TCGA-44-6144 TCGA-55-7907 TCGA-55-8091 TCGA-55-8506 
        5.98        46.98        23.77         0.53        19.73         0.36 
TCGA-55-8614 TCGA-86-7713 TCGA-86-8055 TCGA-93-A4JO TCGA-95-7567 TCGA-L4-A4E5 
       17.62        13.87         4.08         1.08        18.67        19.00 

$`MYO1G WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.37        12.59        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
        0.16        29.72        15.19         3.29        19.66         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
       27.09        12.36         5.88        31.13        34.39        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       19.43        19.89        16.70        24.49         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        4.18         6.12        23.61        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.22         2.86        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        35.47        16.44        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MYO1G MUTATED MYO1G WILD-TYPE 
           0.36            0.00 
  MYO1G MUTATED MYO1G WILD-TYPE 
          46.98          223.96 
  MYO1G MUTATED MYO1G WILD-TYPE 
         15.745          18.100 
[1] "0.4 - 47.0 (15.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D199V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MYO1G MUTATED         1        3        3         3         2          0
  MYO1G WILD-TYPE       3      120      130        43        65         70
                 vv
clus              STAGE IIIB STAGE IV
  MYO1G MUTATED            0        0
  MYO1G WILD-TYPE         11       25
D199V3, multiclass
            clus
vv           MYO1G MUTATED MYO1G WILD-TYPE
  STAGE I                1               3
  STAGE IA               3             120
  STAGE IB               3             130
  STAGE IIA              3              43
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYO1G MUTATED     4   7   1   0
  MYO1G WILD-TYPE 151 254  42  18
D199V4, multiclass
    clus
vv   MYO1G MUTATED MYO1G WILD-TYPE
  T1             4             151
  T2             7             254
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  MYO1G MUTATED     9   3     0
  MYO1G WILD-TYPE 298  86    72
D199V5, multiclass
       clus
vv      MYO1G MUTATED MYO1G WILD-TYPE
  N0                9             298
  N1                3              86
  N2+N3             0              72
[1] 3 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
  MYO1G MUTATED     7   0
  MYO1G WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1G MUTATED      7    0
  MYO1G WILD-TYPE  320   23
   clus
vv  MYO1G MUTATED MYO1G WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D199V7, binary
                 cls
clus                0   1
  MYO1G MUTATED     2  10
  MYO1G WILD-TYPE 257 211
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1G MUTATED      2   10
  MYO1G WILD-TYPE  257  211
        clus
vv       MYO1G MUTATED MYO1G WILD-TYPE
  FEMALE             2             257
  MALE              10             211
[1] 2 2
[1] FALSE
D199V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MYO1G MUTATED                            0                                 2
  MYO1G WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MYO1G MUTATED                                                   10
  MYO1G WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MYO1G MUTATED                                            0
  MYO1G WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MYO1G MUTATED                                               0
  MYO1G WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MYO1G MUTATED                                0
  MYO1G WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MYO1G MUTATED                                    0
  MYO1G WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MYO1G MUTATED                              0                             0
  MYO1G WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MYO1G MUTATED                                               0
  MYO1G WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MYO1G MUTATED                              0
  MYO1G WILD-TYPE                            9
D199V9, multiclass
                                                    clus
vv                                                   MYO1G MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MYO1G WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V10, binary
                 cls
clus                0   1
  MYO1G MUTATED     0  12
  MYO1G WILD-TYPE  20 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1G MUTATED      0   12
  MYO1G WILD-TYPE   20  448
     clus
vv    MYO1G MUTATED MYO1G WILD-TYPE
  NO              0              20
  YES            12             448
[1] 2 2
[1] FALSE
D199V11, continuous
D199V12, continuous
                 vv
clus               R0  R1  R2  RX
  MYO1G MUTATED     8   0   0   2
  MYO1G WILD-TYPE 302  11   4  23
D199V13, multiclass
    clus
vv   MYO1G MUTATED MYO1G WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO1G MUTATED                                  0     0
  MYO1G WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO1G MUTATED                           0    12
  MYO1G WILD-TYPE                        29   365
D199V14, multiclass
                                  clus
vv                                 MYO1G MUTATED MYO1G WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V15, binary
                 cls
clus                0   1
  MYO1G MUTATED     0  12
  MYO1G WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1G MUTATED      0   12
  MYO1G WILD-TYPE    6  337
                        clus
vv                       MYO1G MUTATED MYO1G WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(200) Variable = PUM2 MUTATION ANALYSIS
D200V1, survival
                sevent
clus2              0   1
  PUM2 MUTATED     8   3
  PUM2 WILD-TYPE 307 138
  PUM2 MUTATED PUM2 WILD-TYPE 
            11            445 
  PUM2 MUTATED PUM2 WILD-TYPE 
             3            138 
$`PUM2 MUTATED`
TCGA-44-2656 TCGA-44-A4SS TCGA-50-6594 TCGA-55-7914 TCGA-64-5781 TCGA-69-7765 
       46.98        13.64        12.16         6.15        51.25         5.42 
TCGA-78-7152 TCGA-78-7155 TCGA-91-A4BC TCGA-95-7948 TCGA-NJ-A55A 
       39.52        38.50         1.45        15.65         0.26 

$`PUM2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
        1.45        18.64         0.53         6.48        17.65        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
        5.69        19.27        20.58        35.93        21.90        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.18        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64        29.13         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PUM2 MUTATED PUM2 WILD-TYPE 
          0.26           0.00 
  PUM2 MUTATED PUM2 WILD-TYPE 
         51.25         223.96 
  PUM2 MUTATED PUM2 WILD-TYPE 
         13.64          18.12 
[1] "0.3 - 51.2 (13.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D200V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PUM2 MUTATED         0        1        7         2         0          1
  PUM2 WILD-TYPE       4      122      126        44        67         69
                vv
clus             STAGE IIIB STAGE IV
  PUM2 MUTATED            0        1
  PUM2 WILD-TYPE         11       24
D200V3, multiclass
            clus
vv           PUM2 MUTATED PUM2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              7            126
  STAGE IIA             2             44
  STAGE IIB             0             67
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PUM2 MUTATED     2   8   1   1
  PUM2 WILD-TYPE 153 253  42  17
D200V4, multiclass
    clus
vv   PUM2 MUTATED PUM2 WILD-TYPE
  T1            2            153
  T2            8            253
  T3            1             42
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  PUM2 MUTATED    10   1     1
  PUM2 WILD-TYPE 297  88    71
D200V5, multiclass
       clus
vv      PUM2 MUTATED PUM2 WILD-TYPE
  N0              10            297
  N1               1             88
  N2+N3            1             71
[1] 3 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
  PUM2 MUTATED     8   0
  PUM2 WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      8    0
  PUM2 WILD-TYPE  319   23
   clus
vv  PUM2 MUTATED PUM2 WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D200V7, binary
                cls
clus               0   1
  PUM2 MUTATED     6   6
  PUM2 WILD-TYPE 253 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      6    6
  PUM2 WILD-TYPE  253  215
        clus
vv       PUM2 MUTATED PUM2 WILD-TYPE
  FEMALE            6            253
  MALE              6            215
[1] 2 2
[1] FALSE
D200V8, continuous
[1] "Remove cluster labels:" "PUM2 MUTATED"          
clus
  PUM2 MUTATED PUM2 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PUM2 MUTATED                            0                                 4
  PUM2 WILD-TYPE                         18                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PUM2 MUTATED                                                    8
  PUM2 WILD-TYPE                                                286
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PUM2 MUTATED                                            0
  PUM2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PUM2 MUTATED                                               0
  PUM2 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  PUM2 MUTATED                                0
  PUM2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  PUM2 MUTATED                                    0
  PUM2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PUM2 MUTATED                              0                             0
  PUM2 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PUM2 MUTATED                                               0
  PUM2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  PUM2 MUTATED                              0
  PUM2 WILD-TYPE                            9
D200V9, multiclass
                                                    clus
vv                                                   PUM2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   PUM2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V10, binary
                cls
clus               0   1
  PUM2 MUTATED     0  12
  PUM2 WILD-TYPE  20 448
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      0   12
  PUM2 WILD-TYPE   20  448
     clus
vv    PUM2 MUTATED PUM2 WILD-TYPE
  NO             0             20
  YES           12            448
[1] 2 2
[1] FALSE
D200V11, continuous
D200V12, continuous
                vv
clus              R0  R1  R2  RX
  PUM2 MUTATED     6   0   0   0
  PUM2 WILD-TYPE 304  11   4  25
D200V13, multiclass
    clus
vv   PUM2 MUTATED PUM2 WILD-TYPE
  R0            6            304
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PUM2 MUTATED                                  0     0
  PUM2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PUM2 MUTATED                           2    10
  PUM2 WILD-TYPE                        27   367
D200V14, multiclass
                                  clus
vv                                 PUM2 MUTATED PUM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                      10            367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V15, binary
                cls
clus               0   1
  PUM2 MUTATED     0  10
  PUM2 WILD-TYPE   6 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      0   10
  PUM2 WILD-TYPE    6  339
                        clus
vv                       PUM2 MUTATED PUM2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(201) Variable = C11ORF63 MUTATION ANALYSIS
D201V1, survival
                    sevent
clus2                  0   1
  C11ORF63 MUTATED    13   4
  C11ORF63 WILD-TYPE 302 137
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                17                439 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 4                137 
$`C11ORF63 MUTATED`
TCGA-05-4424 TCGA-38-4628 TCGA-38-4632 TCGA-44-2665 TCGA-44-8117 TCGA-44-8120 
       30.02        49.05        44.61        42.77        12.66         8.55 
TCGA-55-6968 TCGA-55-7994 TCGA-55-8092 TCGA-55-8301 TCGA-55-8616 TCGA-55-A4DG 
       42.51        19.82         5.06         1.45         1.58        19.99 
TCGA-86-8073 TCGA-95-7567 TCGA-97-7547 TCGA-MN-A4N4 TCGA-NJ-A4YP 
       24.33        18.67        64.60        38.63         1.64 

$`C11ORF63 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       37.71        28.41        35.28        11.64        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-3396 TCGA-44-3398 
        4.37        46.98        13.15        24.36        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       17.59        23.64         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
        0.07        32.65         0.79        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
        1.08         1.51         2.17        22.16        15.42         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
        0.10         4.80         6.64        17.62         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 
       20.58        19.59         0.92        15.81        20.19         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
       19.00        17.29         1.12         1.22         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       19.89        31.69        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81         0.20        27.19         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
              1.45               0.00 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             64.60             223.96 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             19.99              17.75 
[1] "1.4 - 64.6 (20.0)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.5"
D201V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C11ORF63 MUTATED         0        2        7         0         6          1
  C11ORF63 WILD-TYPE       4      121      126        46        61         69
                    vv
clus                 STAGE IIIB STAGE IV
  C11ORF63 MUTATED            0        2
  C11ORF63 WILD-TYPE         11       23
D201V3, multiclass
            clus
vv           C11ORF63 MUTATED C11ORF63 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  2                121
  STAGE IB                  7                126
  STAGE IIA                 0                 46
  STAGE IIB                 6                 61
  STAGE IIIA                1                 69
  STAGE IIIB                0                 11
  STAGE IV                  2                 23
[1] 8 2
[1] TRUE
[1] "dimension of 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     3  12   3   0
  C11ORF63 WILD-TYPE 152 249  40  18
D201V4, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  T1                3                152
  T2               12                249
  T3                3                 40
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  C11ORF63 MUTATED    13   4     1
  C11ORF63 WILD-TYPE 294  85    71
D201V5, multiclass
       clus
vv      C11ORF63 MUTATED C11ORF63 WILD-TYPE
  N0                  13                294
  N1                   4                 85
  N2+N3                1                 71
[1] 3 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
  C11ORF63 MUTATED    11   2
  C11ORF63 WILD-TYPE 316  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED     11    2
  C11ORF63 WILD-TYPE  316   21
   clus
vv  C11ORF63 MUTATED C11ORF63 WILD-TYPE
  0               11                316
  1                2                 21
[1] 2 2
[1] FALSE
D201V7, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED     6  12
  C11ORF63 WILD-TYPE 253 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      6   12
  C11ORF63 WILD-TYPE  253  209
        clus
vv       C11ORF63 MUTATED C11ORF63 WILD-TYPE
  FEMALE                6                253
  MALE                 12                209
[1] 2 2
[1] FALSE
D201V8, continuous
[1] "Remove cluster labels:" "C11ORF63 MUTATED"      
clus
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 1                 83 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-7283         TCGA-55-7573 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-55-7725         TCGA-55-7910         TCGA-55-7914 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8096         TCGA-55-8205 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8507         TCGA-55-8508 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8619 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-55-8620         TCGA-55-A48Z         TCGA-55-A490 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-55-A494         TCGA-62-8394         TCGA-62-8395 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-62-8397         TCGA-62-8398         TCGA-62-8399 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-62-8402         TCGA-62-A46O         TCGA-62-A46P 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-62-A46R         TCGA-62-A46S         TCGA-62-A46U 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-62-A46V         TCGA-62-A46Y         TCGA-62-A470 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-62-A471         TCGA-62-A472         TCGA-64-1677 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-64-1681         TCGA-64-5778         TCGA-69-7974 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-69-8254         TCGA-71-6725         TCGA-71-8520 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-73-4659         TCGA-73-4662         TCGA-73-4666 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-73-4668         TCGA-73-4676         TCGA-73-7498 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-73-7499         TCGA-75-5122         TCGA-83-5908 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-86-7701         TCGA-86-7711         TCGA-86-7713 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-86-7714         TCGA-86-7954         TCGA-86-7955 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-86-8055         TCGA-86-8056         TCGA-86-8074 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-86-8075         TCGA-86-8076         TCGA-86-8278 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-86-8279         TCGA-86-8281         TCGA-86-8358 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-86-8359         TCGA-86-8668         TCGA-86-8669 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-86-8671         TCGA-86-A4JF         TCGA-86-A4P7 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-91-6849         TCGA-93-7348         TCGA-93-8067 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-93-A4JN         TCGA-93-A4JO         TCGA-99-7458 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-MN-A4N1         TCGA-MN-A4N5 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  C11ORF63 MUTATED                            0
  C11ORF63 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  C11ORF63 MUTATED                                   2
  C11ORF63 WILD-TYPE                               100
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C11ORF63 MUTATED                                                   13
  C11ORF63 WILD-TYPE                                                281
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C11ORF63 MUTATED                                            0
  C11ORF63 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C11ORF63 MUTATED                                               1
  C11ORF63 WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  C11ORF63 MUTATED                                0
  C11ORF63 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  C11ORF63 MUTATED                                    0
  C11ORF63 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C11ORF63 MUTATED                              0                             2
  C11ORF63 WILD-TYPE                            2                            20
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C11ORF63 MUTATED                                               0
  C11ORF63 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  C11ORF63 MUTATED                              0
  C11ORF63 WILD-TYPE                            9
D201V9, multiclass
                                                    clus
vv                                                   C11ORF63 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   C11ORF63 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V10, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED     0  18
  C11ORF63 WILD-TYPE  20 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      0   18
  C11ORF63 WILD-TYPE   20  442
     clus
vv    C11ORF63 MUTATED C11ORF63 WILD-TYPE
  NO                 0                 20
  YES               18                442
[1] 2 2
[1] FALSE
D201V11, continuous
D201V12, continuous
                    vv
clus                  R0  R1  R2  RX
  C11ORF63 MUTATED    11   1   0   0
  C11ORF63 WILD-TYPE 299  10   4  25
D201V13, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  R0               11                299
  R1                1                 10
  R2                0                  4
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C11ORF63 MUTATED                                  0     0
  C11ORF63 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C11ORF63 MUTATED                           2    14
  C11ORF63 WILD-TYPE                        27   363
D201V14, multiclass
                                  clus
vv                                 C11ORF63 MUTATED C11ORF63 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       2                 27
  WHITE                                          14                363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V15, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED     0  16
  C11ORF63 WILD-TYPE   6 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      0   16
  C11ORF63 WILD-TYPE    6  333
                        clus
vv                       C11ORF63 MUTATED C11ORF63 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               16                333
[1] 2 2
[1] FALSE

Clustering(202) Variable = IPP MUTATION ANALYSIS
D202V1, survival
               sevent
clus2             0   1
  IPP MUTATED     2   3
  IPP WILD-TYPE 313 138
  IPP MUTATED IPP WILD-TYPE 
            5           451 
  IPP MUTATED IPP WILD-TYPE 
            3           138 
$`IPP MUTATED`
TCGA-05-4398 TCGA-38-7271 TCGA-44-7660 TCGA-53-7624 TCGA-55-A4DF 
       47.05        26.30        19.46        34.29        20.19 

$`IPP WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        14.60        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
        1.58        20.58        19.59         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  IPP MUTATED IPP WILD-TYPE 
        19.46          0.00 
  IPP MUTATED IPP WILD-TYPE 
        47.05        223.96 
  IPP MUTATED IPP WILD-TYPE 
        26.30         17.75 
[1] "19.5 - 47.0 (26.3)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.6"
D202V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IPP MUTATED         0        2        1         0         0          0
  IPP WILD-TYPE       4      121      132        46        67         70
               vv
clus            STAGE IIIB STAGE IV
  IPP MUTATED            1        1
  IPP WILD-TYPE         10       24
D202V3, multiclass
            clus
vv           IPP MUTATED IPP WILD-TYPE
  STAGE I              0             4
  STAGE IA             2           121
  STAGE IB             1           132
  STAGE IIA            0            46
  STAGE IIB            0            67
  STAGE IIIA           0            70
  STAGE IIIB           1            10
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IPP MUTATED     2   2   0   1
  IPP WILD-TYPE 153 259  43  17
D202V4, multiclass
    clus
vv   IPP MUTATED IPP WILD-TYPE
  T1           2           153
  T2           2           259
  T3           0            43
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  IPP MUTATED     4   0     1
  IPP WILD-TYPE 303  89    71
D202V5, multiclass
       clus
vv      IPP MUTATED IPP WILD-TYPE
  N0              4           303
  N1              0            89
  N2+N3           1            71
[1] 3 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
  IPP MUTATED     2   1
  IPP WILD-TYPE 325  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      2    1
  IPP WILD-TYPE  325   22
   clus
vv  IPP MUTATED IPP WILD-TYPE
  0           2           325
  1           1            22
[1] 2 2
[1] FALSE
D202V7, binary
               cls
clus              0   1
  IPP MUTATED     3   2
  IPP WILD-TYPE 256 219
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      3    2
  IPP WILD-TYPE  256  219
        clus
vv       IPP MUTATED IPP WILD-TYPE
  FEMALE           3           256
  MALE             2           219
[1] 2 2
[1] FALSE
D202V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  IPP MUTATED                            0                                 1
  IPP WILD-TYPE                         18                               101
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IPP MUTATED                                                    4
  IPP WILD-TYPE                                                290
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IPP MUTATED                                            0
  IPP WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IPP MUTATED                                               0
  IPP WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  IPP MUTATED                                0
  IPP WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  IPP MUTATED                                    0                            0
  IPP WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  IPP MUTATED                               0
  IPP WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IPP MUTATED                                               0
  IPP WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  IPP MUTATED                              0
  IPP WILD-TYPE                            9
D202V9, multiclass
                                                    clus
vv                                                   IPP MUTATED IPP WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            1           101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           4           290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V10, binary
               cls
clus              0   1
  IPP MUTATED     0   5
  IPP WILD-TYPE  20 455
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      0    5
  IPP WILD-TYPE   20  455
     clus
vv    IPP MUTATED IPP WILD-TYPE
  NO            0            20
  YES           5           455
[1] 2 2
[1] FALSE
D202V11, continuous
D202V12, continuous
               vv
clus             R0  R1  R2  RX
  IPP MUTATED     4   0   0   0
  IPP WILD-TYPE 306  11   4  25
D202V13, multiclass
    clus
vv   IPP MUTATED IPP WILD-TYPE
  R0           4           306
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IPP MUTATED                                  0     0
  IPP WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IPP MUTATED                           0     4
  IPP WILD-TYPE                        29   373
D202V14, multiclass
                                  clus
vv                                 IPP MUTATED IPP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                      4           373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V15, binary
               cls
clus              0   1
  IPP MUTATED     1   3
  IPP WILD-TYPE   5 346
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      1    3
  IPP WILD-TYPE    5  346
                        clus
vv                       IPP MUTATED IPP WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO           3           346
[1] 2 2
[1] FALSE

Clustering(203) Variable = XRCC6 MUTATION ANALYSIS
D203V1, survival
                 sevent
clus2               0   1
  XRCC6 MUTATED     5   2
  XRCC6 WILD-TYPE 310 139
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              7             449 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              2             139 
$`XRCC6 MUTATED`
TCGA-55-A491 TCGA-64-5781 TCGA-73-4666 TCGA-78-7150 TCGA-78-7156 TCGA-86-8073 
       20.58        51.25        26.30        21.90        32.09        24.33 
TCGA-93-8067 
        6.12 

$`XRCC6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
       16.93        22.65        20.71        21.40         1.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        42.90        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       35.93        39.52        24.99        19.50        38.50         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  XRCC6 MUTATED XRCC6 WILD-TYPE 
           6.12            0.00 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
          51.25          223.96 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
          24.33           17.75 
[1] "6.1 - 51.2 (24.3)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.2"
D203V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  XRCC6 MUTATED         0        1        3         0         2          0
  XRCC6 WILD-TYPE       4      122      130        46        65         70
                 vv
clus              STAGE IIIB STAGE IV
  XRCC6 MUTATED            0        2
  XRCC6 WILD-TYPE         11       23
D203V3, multiclass
            clus
vv           XRCC6 MUTATED XRCC6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XRCC6 MUTATED     2   5   0   1
  XRCC6 WILD-TYPE 153 256  43  17
D203V4, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  T1             2             153
  T2             5             256
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  XRCC6 MUTATED     5   3     0
  XRCC6 WILD-TYPE 302  86    72
D203V5, multiclass
       clus
vv      XRCC6 MUTATED XRCC6 WILD-TYPE
  N0                5             302
  N1                3              86
  N2+N3             0              72
[1] 3 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
  XRCC6 MUTATED     4   2
  XRCC6 WILD-TYPE 323  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      4    2
  XRCC6 WILD-TYPE  323   21
   clus
vv  XRCC6 MUTATED XRCC6 WILD-TYPE
  0             4             323
  1             2              21
[1] 2 2
[1] FALSE
D203V7, binary
                 cls
clus                0   1
  XRCC6 MUTATED     3   5
  XRCC6 WILD-TYPE 256 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      3    5
  XRCC6 WILD-TYPE  256  216
        clus
vv       XRCC6 MUTATED XRCC6 WILD-TYPE
  FEMALE             3             256
  MALE               5             216
[1] 2 2
[1] FALSE
D203V8, continuous
[1] "Remove cluster labels:" "XRCC6 MUTATED"         
clus
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4668 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"XRCC6 WILD-TYPE" "XRCC6 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  XRCC6 MUTATED                            0                                 2
  XRCC6 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XRCC6 MUTATED                                                    5
  XRCC6 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XRCC6 MUTATED                                            0
  XRCC6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  XRCC6 MUTATED                                               1
  XRCC6 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  XRCC6 MUTATED                                0
  XRCC6 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  XRCC6 MUTATED                                    0
  XRCC6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  XRCC6 MUTATED                              0                             0
  XRCC6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  XRCC6 MUTATED                                               0
  XRCC6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  XRCC6 MUTATED                              0
  XRCC6 WILD-TYPE                            9
D203V9, multiclass
                                                    clus
vv                                                   XRCC6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   XRCC6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V10, binary
                 cls
clus                0   1
  XRCC6 MUTATED     1   7
  XRCC6 WILD-TYPE  19 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      1    7
  XRCC6 WILD-TYPE   19  453
     clus
vv    XRCC6 MUTATED XRCC6 WILD-TYPE
  NO              1              19
  YES             7             453
[1] 2 2
[1] FALSE
D203V11, continuous
D203V12, continuous
                 vv
clus               R0  R1  R2  RX
  XRCC6 MUTATED     7   0   0   1
  XRCC6 WILD-TYPE 303  11   4  24
D203V13, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XRCC6 MUTATED                                  0     1
  XRCC6 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  XRCC6 MUTATED                           0     6
  XRCC6 WILD-TYPE                        29   371
D203V14, multiclass
                                  clus
vv                                 XRCC6 MUTATED XRCC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V15, binary
                 cls
clus                0   1
  XRCC6 MUTATED     0   5
  XRCC6 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      0    5
  XRCC6 WILD-TYPE    6  344
                        clus
vv                       XRCC6 MUTATED XRCC6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(204) Variable = RHEB MUTATION ANALYSIS
D204V1, survival
                sevent
clus2              0   1
  RHEB MUTATED     0   4
  RHEB WILD-TYPE 315 137
  RHEB MUTATED RHEB WILD-TYPE 
             4            452 
  RHEB MUTATED RHEB WILD-TYPE 
             4            137 
$`RHEB MUTATED`
TCGA-05-4250 TCGA-38-4631 TCGA-64-1677 TCGA-73-4659 
        3.98        11.64        20.65        23.38 

$`RHEB WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01         0.10        52.60        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  RHEB MUTATED RHEB WILD-TYPE 
          3.98           0.00 
  RHEB MUTATED RHEB WILD-TYPE 
         23.38         223.96 
  RHEB MUTATED RHEB WILD-TYPE 
        16.145         18.030 
[1] "4.0 - 23.4 (16.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "6.2"
D204V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RHEB MUTATED         0        0        1         0         0          3
  RHEB WILD-TYPE       4      123      132        46        67         67
                vv
clus             STAGE IIIB STAGE IV
  RHEB MUTATED            0        0
  RHEB WILD-TYPE         11       25
D204V3, multiclass
            clus
vv           RHEB MUTATED RHEB WILD-TYPE
  STAGE I               0              4
  STAGE IA              0            123
  STAGE IB              1            132
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            3             67
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHEB MUTATED     0   3   1   0
  RHEB WILD-TYPE 155 258  42  18
D204V4, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  T1            0            155
  T2            3            258
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  RHEB MUTATED     1   1     2
  RHEB WILD-TYPE 306  88    70
D204V5, multiclass
       clus
vv      RHEB MUTATED RHEB WILD-TYPE
  N0               1            306
  N1               1             88
  N2+N3            2             70
[1] 3 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
  RHEB MUTATED     4   0
  RHEB WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      4    0
  RHEB WILD-TYPE  323   23
   clus
vv  RHEB MUTATED RHEB WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D204V7, binary
                cls
clus               0   1
  RHEB MUTATED     3   1
  RHEB WILD-TYPE 256 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      3    1
  RHEB WILD-TYPE  256  220
        clus
vv       RHEB MUTATED RHEB WILD-TYPE
  FEMALE            3            256
  MALE              1            220
[1] 2 2
[1] FALSE
D204V8, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1681     TCGA-64-5778 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4676 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8055     TCGA-86-8056 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RHEB MUTATED                            0                                 0
  RHEB WILD-TYPE                         18                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RHEB MUTATED                                                    4
  RHEB WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RHEB MUTATED                                            0
  RHEB WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RHEB MUTATED                                               0
  RHEB WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RHEB MUTATED                                0
  RHEB WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RHEB MUTATED                                    0
  RHEB WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RHEB MUTATED                              0                             0
  RHEB WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RHEB MUTATED                                               0
  RHEB WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RHEB MUTATED                              0
  RHEB WILD-TYPE                            9
D204V9, multiclass
                                                    clus
vv                                                   RHEB MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RHEB WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V10, binary
                cls
clus               0   1
  RHEB MUTATED     0   4
  RHEB WILD-TYPE  20 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      0    4
  RHEB WILD-TYPE   20  456
     clus
vv    RHEB MUTATED RHEB WILD-TYPE
  NO             0             20
  YES            4            456
[1] 2 2
[1] FALSE
D204V11, continuous
D204V12, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     TCGA-44-3396 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-5644 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6147 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     TCGA-44-6776 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7661     TCGA-44-7662     TCGA-44-7667 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7670     TCGA-44-7672     TCGA-44-8117 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-1592     TCGA-55-1595     TCGA-55-5899     TCGA-55-6642 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-6712     TCGA-55-6971     TCGA-55-7227     TCGA-55-7283 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7728     TCGA-55-7907 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7914     TCGA-55-8089 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8615     TCGA-55-8620     TCGA-55-8621 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A493     TCGA-55-A494 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-62-8398     TCGA-64-1681     TCGA-64-5774     TCGA-64-5775 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5779     TCGA-64-5781     TCGA-69-7761 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-69-7763     TCGA-69-7764     TCGA-69-7765     TCGA-69-7974 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-69-7979     TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-7498     TCGA-75-6214 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-75-7025     TCGA-75-7027     TCGA-75-7031     TCGA-78-7145 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7542 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6851     TCGA-86-7711     TCGA-86-7714 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-7954     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6836 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  RHEB MUTATED     3   0   1   0
  RHEB WILD-TYPE 307  11   3  25
D204V13, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  R0            3            307
  R1            0             11
  R2            1              3
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHEB MUTATED                                  0     0
  RHEB WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHEB MUTATED                           0     3
  RHEB WILD-TYPE                        29   374
D204V14, multiclass
                                  clus
vv                                 RHEB MUTATED RHEB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       3            374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V15, binary
                cls
clus               0   1
  RHEB MUTATED     0   3
  RHEB WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      0    3
  RHEB WILD-TYPE    6  346
                        clus
vv                       RHEB MUTATED RHEB WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(205) Variable = TSLP MUTATION ANALYSIS
D205V1, survival
                sevent
clus2              0   1
  TSLP MUTATED     5   2
  TSLP WILD-TYPE 310 139
  TSLP MUTATED TSLP WILD-TYPE 
             7            449 
  TSLP MUTATED TSLP WILD-TYPE 
             2            139 
$`TSLP MUTATED`
TCGA-05-4430 TCGA-38-4631 TCGA-44-7671 TCGA-55-7994 TCGA-62-8394 TCGA-86-6851 
       25.02        11.64        17.59        19.82         4.57         5.88 
TCGA-99-8033 
        5.59 

$`TSLP WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       19.99        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  TSLP MUTATED TSLP WILD-TYPE 
          4.57           0.00 
  TSLP MUTATED TSLP WILD-TYPE 
         25.02         223.96 
  TSLP MUTATED TSLP WILD-TYPE 
         11.64          18.12 
[1] "4.6 - 25.0 (11.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.1"
D205V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TSLP MUTATED         0        0        3         1         1          0
  TSLP WILD-TYPE       4      123      130        45        66         70
                vv
clus             STAGE IIIB STAGE IV
  TSLP MUTATED            1        1
  TSLP WILD-TYPE         10       24
D205V3, multiclass
            clus
vv           TSLP MUTATED TSLP WILD-TYPE
  STAGE I               0              4
  STAGE IA              0            123
  STAGE IB              3            130
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TSLP MUTATED     1   3   1   1
  TSLP WILD-TYPE 154 258  42  17
D205V4, multiclass
    clus
vv   TSLP MUTATED TSLP WILD-TYPE
  T1            1            154
  T2            3            258
  T3            1             42
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  TSLP MUTATED     4   1     1
  TSLP WILD-TYPE 303  88    71
D205V5, multiclass
       clus
vv      TSLP MUTATED TSLP WILD-TYPE
  N0               4            303
  N1               1             88
  N2+N3            1             71
[1] 3 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
  TSLP MUTATED     5   1
  TSLP WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSLP MUTATED      5    1
  TSLP WILD-TYPE  322   22
   clus
vv  TSLP MUTATED TSLP WILD-TYPE
  0            5            322
  1            1             22
[1] 2 2
[1] FALSE
D205V7, binary
                cls
clus               0   1
  TSLP MUTATED     5   2
  TSLP WILD-TYPE 254 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSLP MUTATED      5    2
  TSLP WILD-TYPE  254  219
        clus
vv       TSLP MUTATED TSLP WILD-TYPE
  FEMALE            5            254
  MALE              2            219
[1] 2 2
[1] FALSE
D205V8, continuous
[1] "Remove cluster labels:" "TSLP MUTATED"          
clus
  TSLP MUTATED TSLP WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8395     TCGA-62-8397 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TSLP MUTATED                            0                                 4
  TSLP WILD-TYPE                         18                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TSLP MUTATED                                                    3
  TSLP WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TSLP MUTATED                                            0
  TSLP WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TSLP MUTATED                                               0
  TSLP WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  TSLP MUTATED                                0
  TSLP WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  TSLP MUTATED                                    0
  TSLP WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TSLP MUTATED                              0                             0
  TSLP WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TSLP MUTATED                                               0
  TSLP WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  TSLP MUTATED                              0
  TSLP WILD-TYPE                            9
D205V9, multiclass
                                                    clus
vv                                                   TSLP MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   TSLP WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V10, binary
                cls
clus               0   1
  TSLP MUTATED     0   7
  TSLP WILD-TYPE  20 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSLP MUTATED      0    7
  TSLP WILD-TYPE   20  453
     clus
vv    TSLP MUTATED TSLP WILD-TYPE
  NO             0             20
  YES            7            453
[1] 2 2
[1] FALSE
D205V11, continuous
D205V12, continuous
[1] "Remove cluster labels:" "TSLP MUTATED"          
clus
  TSLP MUTATED TSLP WILD-TYPE 
             1            256 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     TCGA-44-3396 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-5644 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6147 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     TCGA-44-6776 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7661     TCGA-44-7662     TCGA-44-7667 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7670     TCGA-44-7672     TCGA-44-8117 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-1592     TCGA-55-1595     TCGA-55-5899     TCGA-55-6642 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-6712     TCGA-55-6971     TCGA-55-7227     TCGA-55-7283 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7728     TCGA-55-7907 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7914     TCGA-55-8089 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8615     TCGA-55-8620     TCGA-55-8621 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A493     TCGA-55-A494 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-62-8398     TCGA-64-1677     TCGA-64-1681     TCGA-64-5774 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-69-7761     TCGA-69-7763     TCGA-69-7764     TCGA-69-7765 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-69-7974     TCGA-69-7979     TCGA-69-8253     TCGA-69-8255 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-69-A59K     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4675     TCGA-73-4676 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-73-7498     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7145     TCGA-78-7146     TCGA-78-7147 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-78-7148     TCGA-78-7149     TCGA-78-7150     TCGA-78-7152 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-78-7153     TCGA-78-7154     TCGA-78-7155     TCGA-78-7156 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-78-7158     TCGA-78-7159     TCGA-78-7160     TCGA-78-7161 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-78-7162     TCGA-78-7163     TCGA-78-7166     TCGA-78-7167 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7542     TCGA-78-7633     TCGA-78-8640 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-78-8648     TCGA-78-8655     TCGA-78-8660     TCGA-78-8662 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-80-5607     TCGA-80-5608     TCGA-83-5908     TCGA-86-7711 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-8054     TCGA-86-8055 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8281 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8669     TCGA-86-8673 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-91-6829     TCGA-91-6830 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-91-6836     TCGA-91-6840     TCGA-91-6849     TCGA-91-8499 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-91-A4BC     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7567     TCGA-95-7944     TCGA-95-7947 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-95-7948     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7553     TCGA-97-7554     TCGA-97-7941 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-97-8171     TCGA-97-8172     TCGA-97-8174     TCGA-97-8176 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-97-8179     TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-99-7458     TCGA-99-8025     TCGA-99-8028     TCGA-99-8032 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-J2-8194     TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-L4-A4E6     TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
    TCGA-MP-A5C7     TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" "TSLP WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  TSLP MUTATED     5   0   0   0
  TSLP WILD-TYPE 305  11   4  25
D205V13, multiclass
    clus
vv   TSLP MUTATED TSLP WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSLP MUTATED                                  0     0
  TSLP WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSLP MUTATED                           1     5
  TSLP WILD-TYPE                        28   372
D205V14, multiclass
                                  clus
vv                                 TSLP MUTATED TSLP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V15, binary
                cls
clus               0   1
  TSLP MUTATED     0   6
  TSLP WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSLP MUTATED      0    6
  TSLP WILD-TYPE    6  343
                        clus
vv                       TSLP MUTATED TSLP WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(206) Variable = LIPG MUTATION ANALYSIS
D206V1, survival
                sevent
clus2              0   1
  LIPG MUTATED     8   1
  LIPG WILD-TYPE 307 140
  LIPG MUTATED LIPG WILD-TYPE 
             9            447 
  LIPG MUTATED LIPG WILD-TYPE 
             1            140 
$`LIPG MUTATED`
TCGA-05-4390 TCGA-49-4507 TCGA-55-8506 TCGA-55-A494 TCGA-69-7980 TCGA-86-6851 
       37.02         8.81         0.36        15.81        12.56         5.88 
TCGA-86-8073 TCGA-95-7947 TCGA-97-7547 
       24.33        15.68        64.60 

$`LIPG WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       12.66        35.54        46.72        14.07        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59         0.92        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       19.89        31.69        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  LIPG MUTATED LIPG WILD-TYPE 
          0.36           0.00 
  LIPG MUTATED LIPG WILD-TYPE 
         64.60         223.96 
  LIPG MUTATED LIPG WILD-TYPE 
         15.68          18.12 
[1] "0.4 - 64.6 (15.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.5"
D206V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LIPG MUTATED         1        1        4         1         1          1
  LIPG WILD-TYPE       3      122      129        45        66         69
                vv
clus             STAGE IIIB STAGE IV
  LIPG MUTATED            0        0
  LIPG WILD-TYPE         11       25
D206V3, multiclass
            clus
vv           LIPG MUTATED LIPG WILD-TYPE
  STAGE I               1              3
  STAGE IA              1            122
  STAGE IB              4            129
  STAGE IIA             1             45
  STAGE IIB             1             66
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIPG MUTATED     3   4   2   0
  LIPG WILD-TYPE 152 257  41  18
D206V4, multiclass
    clus
vv   LIPG MUTATED LIPG WILD-TYPE
  T1            3            152
  T2            4            257
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  LIPG MUTATED     7   2     0
  LIPG WILD-TYPE 300  87    72
D206V5, multiclass
       clus
vv      LIPG MUTATED LIPG WILD-TYPE
  N0               7            300
  N1               2             87
  N2+N3            0             72
[1] 3 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
  LIPG MUTATED     6   0
  LIPG WILD-TYPE 321  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPG MUTATED      6    0
  LIPG WILD-TYPE  321   23
   clus
vv  LIPG MUTATED LIPG WILD-TYPE
  0            6            321
  1            0             23
[1] 2 2
[1] FALSE
D206V7, binary
                cls
clus               0   1
  LIPG MUTATED     7   2
  LIPG WILD-TYPE 252 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPG MUTATED      7    2
  LIPG WILD-TYPE  252  219
        clus
vv       LIPG MUTATED LIPG WILD-TYPE
  FEMALE            7            252
  MALE              2            219
[1] 2 2
[1] FALSE
D206V8, continuous
[1] "Remove cluster labels:" "LIPG MUTATED"          
clus
  LIPG MUTATED LIPG WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-55-A490     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"LIPG WILD-TYPE" "LIPG WILD-TYPE" "LIPG WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LIPG MUTATED                            0                                 3
  LIPG WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LIPG MUTATED                                                    4
  LIPG WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LIPG MUTATED                                            0
  LIPG WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LIPG MUTATED                                               1
  LIPG WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  LIPG MUTATED                                0
  LIPG WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  LIPG MUTATED                                    0
  LIPG WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LIPG MUTATED                              0                             1
  LIPG WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LIPG MUTATED                                               0
  LIPG WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  LIPG MUTATED                              0
  LIPG WILD-TYPE                            9
D206V9, multiclass
                                                    clus
vv                                                   LIPG MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   LIPG WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V10, binary
                cls
clus               0   1
  LIPG MUTATED     1   8
  LIPG WILD-TYPE  19 452
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPG MUTATED      1    8
  LIPG WILD-TYPE   19  452
     clus
vv    LIPG MUTATED LIPG WILD-TYPE
  NO             1             19
  YES            8            452
[1] 2 2
[1] FALSE
D206V11, continuous
D206V12, continuous
                vv
clus              R0  R1  R2  RX
  LIPG MUTATED     6   0   0   0
  LIPG WILD-TYPE 304  11   4  25
D206V13, multiclass
    clus
vv   LIPG MUTATED LIPG WILD-TYPE
  R0            6            304
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIPG MUTATED                                  0     0
  LIPG WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIPG MUTATED                           0     8
  LIPG WILD-TYPE                        29   369
D206V14, multiclass
                                  clus
vv                                 LIPG MUTATED LIPG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V15, binary
                cls
clus               0   1
  LIPG MUTATED     0   8
  LIPG WILD-TYPE   6 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPG MUTATED      0    8
  LIPG WILD-TYPE    6  341
                        clus
vv                       LIPG MUTATED LIPG WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(207) Variable = SOS1 MUTATION ANALYSIS
D207V1, survival
                sevent
clus2              0   1
  SOS1 MUTATED    11   2
  SOS1 WILD-TYPE 304 139
  SOS1 MUTATED SOS1 WILD-TYPE 
            13            443 
  SOS1 MUTATED SOS1 WILD-TYPE 
             2            139 
$`SOS1 MUTATED`
TCGA-05-4396 TCGA-44-2665 TCGA-44-3918 TCGA-44-7667 TCGA-44-A4SS TCGA-49-6745 
        9.96        42.77        34.06        36.07        13.64        17.16 
TCGA-50-5068 TCGA-55-7994 TCGA-55-8089 TCGA-67-3771 TCGA-78-7152 TCGA-95-7948 
       49.28        19.82         3.29        20.05        39.52        15.65 
TCGA-97-A4M3 
       17.75 

$`SOS1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
       14.60        19.46        12.03         7.17        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       12.13        29.26        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
       70.55        15.72        60.16        31.04         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
       17.65         6.15         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.68        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  SOS1 MUTATED SOS1 WILD-TYPE 
          3.29           0.00 
  SOS1 MUTATED SOS1 WILD-TYPE 
         49.28         223.96 
  SOS1 MUTATED SOS1 WILD-TYPE 
         19.82          17.98 
[1] "3.3 - 49.3 (19.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.2"
D207V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SOS1 MUTATED         0        5        2         0         4          2
  SOS1 WILD-TYPE       4      118      131        46        63         68
                vv
clus             STAGE IIIB STAGE IV
  SOS1 MUTATED            1        0
  SOS1 WILD-TYPE         10       25
D207V3, multiclass
            clus
vv           SOS1 MUTATED SOS1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              5            118
  STAGE IB              2            131
  STAGE IIA             0             46
  STAGE IIB             4             63
  STAGE IIIA            2             68
  STAGE IIIB            1             10
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOS1 MUTATED     5   6   2   1
  SOS1 WILD-TYPE 150 255  41  17
D207V4, multiclass
    clus
vv   SOS1 MUTATED SOS1 WILD-TYPE
  T1            5            150
  T2            6            255
  T3            2             41
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  SOS1 MUTATED     9   3     2
  SOS1 WILD-TYPE 298  86    70
D207V5, multiclass
       clus
vv      SOS1 MUTATED SOS1 WILD-TYPE
  N0               9            298
  N1               3             86
  N2+N3            2             70
[1] 3 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
  SOS1 MUTATED    11   0
  SOS1 WILD-TYPE 316  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED     11    0
  SOS1 WILD-TYPE  316   23
   clus
vv  SOS1 MUTATED SOS1 WILD-TYPE
  0           11            316
  1            0             23
[1] 2 2
[1] FALSE
D207V7, binary
                cls
clus               0   1
  SOS1 MUTATED     8   6
  SOS1 WILD-TYPE 251 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      8    6
  SOS1 WILD-TYPE  251  215
        clus
vv       SOS1 MUTATED SOS1 WILD-TYPE
  FEMALE            8            251
  MALE              6            215
[1] 2 2
[1] FALSE
D207V8, continuous
[1] "Remove cluster labels:" "SOS1 MUTATED"          
clus
  SOS1 MUTATED SOS1 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"SOS1 WILD-TYPE" "SOS1 WILD-TYPE" "SOS1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SOS1 MUTATED                            0                                 4
  SOS1 WILD-TYPE                         18                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SOS1 MUTATED                                                   10
  SOS1 WILD-TYPE                                                284
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SOS1 MUTATED                                            0
  SOS1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SOS1 MUTATED                                               0
  SOS1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SOS1 MUTATED                                0
  SOS1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SOS1 MUTATED                                    0
  SOS1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SOS1 MUTATED                              0                             0
  SOS1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SOS1 MUTATED                                               0
  SOS1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SOS1 MUTATED                              0
  SOS1 WILD-TYPE                            9
D207V9, multiclass
                                                    clus
vv                                                   SOS1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SOS1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V10, binary
                cls
clus               0   1
  SOS1 MUTATED     0  14
  SOS1 WILD-TYPE  20 446
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      0   14
  SOS1 WILD-TYPE   20  446
     clus
vv    SOS1 MUTATED SOS1 WILD-TYPE
  NO             0             20
  YES           14            446
[1] 2 2
[1] FALSE
D207V11, continuous
D207V12, continuous
                vv
clus              R0  R1  R2  RX
  SOS1 MUTATED     9   0   0   0
  SOS1 WILD-TYPE 301  11   4  25
D207V13, multiclass
    clus
vv   SOS1 MUTATED SOS1 WILD-TYPE
  R0            9            301
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOS1 MUTATED                                  0     0
  SOS1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SOS1 MUTATED                           1    11
  SOS1 WILD-TYPE                        28   366
D207V14, multiclass
                                  clus
vv                                 SOS1 MUTATED SOS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      11            366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V15, binary
                cls
clus               0   1
  SOS1 MUTATED     0  10
  SOS1 WILD-TYPE   6 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      0   10
  SOS1 WILD-TYPE    6  339
                        clus
vv                       SOS1 MUTATED SOS1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(208) Variable = KCTD1 MUTATION ANALYSIS
D208V1, survival
                 sevent
clus2               0   1
  KCTD1 MUTATED     4   2
  KCTD1 WILD-TYPE 311 139
  KCTD1 MUTATED KCTD1 WILD-TYPE 
              6             450 
  KCTD1 MUTATED KCTD1 WILD-TYPE 
              2             139 
$`KCTD1 MUTATED`
TCGA-44-A47G TCGA-49-4506 TCGA-55-7281 TCGA-78-7155 TCGA-86-8076 TCGA-91-6831 
       11.54        32.84         0.59        38.50        16.08        10.19 

$`KCTD1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.08        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        46.72        14.07         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       15.75        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  KCTD1 MUTATED KCTD1 WILD-TYPE 
           0.59            0.00 
  KCTD1 MUTATED KCTD1 WILD-TYPE 
          38.50          223.96 
  KCTD1 MUTATED KCTD1 WILD-TYPE 
          13.81           18.10 
[1] "0.6 - 38.5 (13.8)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D208V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KCTD1 MUTATED         0        3        2         0         1          0
  KCTD1 WILD-TYPE       4      120      131        46        66         70
                 vv
clus              STAGE IIIB STAGE IV
  KCTD1 MUTATED            0        0
  KCTD1 WILD-TYPE         11       25
D208V3, multiclass
            clus
vv           KCTD1 MUTATED KCTD1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               2             131
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCTD1 MUTATED     3   3   0   0
  KCTD1 WILD-TYPE 152 258  43  18
D208V4, multiclass
    clus
vv   KCTD1 MUTATED KCTD1 WILD-TYPE
  T1             3             152
  T2             3             258
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  KCTD1 MUTATED     5   1     0
  KCTD1 WILD-TYPE 302  88    72
D208V5, multiclass
       clus
vv      KCTD1 MUTATED KCTD1 WILD-TYPE
  N0                5             302
  N1                1              88
  N2+N3             0              72
[1] 3 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
  KCTD1 MUTATED     5   0
  KCTD1 WILD-TYPE 322  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD1 MUTATED      5    0
  KCTD1 WILD-TYPE  322   23
   clus
vv  KCTD1 MUTATED KCTD1 WILD-TYPE
  0             5             322
  1             0              23
[1] 2 2
[1] FALSE
D208V7, binary
                 cls
clus                0   1
  KCTD1 MUTATED     3   3
  KCTD1 WILD-TYPE 256 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD1 MUTATED      3    3
  KCTD1 WILD-TYPE  256  218
        clus
vv       KCTD1 MUTATED KCTD1 WILD-TYPE
  FEMALE             3             256
  MALE               3             218
[1] 2 2
[1] FALSE
D208V8, continuous
[1] "Remove cluster labels:" "KCTD1 MUTATED"         
clus
  KCTD1 MUTATED KCTD1 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KCTD1 MUTATED                            0                                 0
  KCTD1 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KCTD1 MUTATED                                                    5
  KCTD1 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KCTD1 MUTATED                                            0
  KCTD1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KCTD1 MUTATED                                               0
  KCTD1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KCTD1 MUTATED                                0
  KCTD1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KCTD1 MUTATED                                    0
  KCTD1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KCTD1 MUTATED                              0                             1
  KCTD1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KCTD1 MUTATED                                               0
  KCTD1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KCTD1 MUTATED                              0
  KCTD1 WILD-TYPE                            9
D208V9, multiclass
                                                    clus
vv                                                   KCTD1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   KCTD1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V10, binary
                 cls
clus                0   1
  KCTD1 MUTATED     0   6
  KCTD1 WILD-TYPE  20 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD1 MUTATED      0    6
  KCTD1 WILD-TYPE   20  454
     clus
vv    KCTD1 MUTATED KCTD1 WILD-TYPE
  NO              0              20
  YES             6             454
[1] 2 2
[1] FALSE
D208V11, continuous
D208V12, continuous
[1] "Remove cluster labels:" "KCTD1 MUTATED"         
clus
  KCTD1 MUTATED KCTD1 WILD-TYPE 
              2             255 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A4SS      TCGA-44-A4SU 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4494      TCGA-49-4505      TCGA-53-7624 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ      TCGA-55-1592 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-1595      TCGA-55-5899      TCGA-55-6642      TCGA-55-6712 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-6971      TCGA-55-7227      TCGA-55-7283      TCGA-55-7570 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7576      TCGA-55-7724      TCGA-55-7725 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-7726      TCGA-55-7728      TCGA-55-7907      TCGA-55-7910 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-7911      TCGA-55-7914      TCGA-55-8089      TCGA-55-8092 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-8094      TCGA-55-8096      TCGA-55-8097      TCGA-55-8205 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-8299      TCGA-55-8301      TCGA-55-8302      TCGA-55-8506 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8511      TCGA-55-8512      TCGA-55-8514 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-8615      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-62-8398 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5774      TCGA-64-5775 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-64-5778      TCGA-64-5779      TCGA-64-5781      TCGA-69-7761 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-69-7763      TCGA-69-7764      TCGA-69-7765      TCGA-69-7974 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-69-7979      TCGA-69-8253      TCGA-69-8255      TCGA-69-A59K 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-73-4670      TCGA-73-4675      TCGA-73-4676      TCGA-73-7498 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7031 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7156      TCGA-78-7158      TCGA-78-7159 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-7160      TCGA-78-7161      TCGA-78-7162      TCGA-78-7163 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-7166      TCGA-78-7167      TCGA-78-7220      TCGA-78-7535 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-7536      TCGA-78-7537      TCGA-78-7539      TCGA-78-7542 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-7633      TCGA-78-8640      TCGA-78-8648      TCGA-78-8655 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-78-8660      TCGA-78-8662      TCGA-80-5607      TCGA-80-5608 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6851      TCGA-86-7711      TCGA-86-7714 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8281      TCGA-86-8358 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8669      TCGA-86-8673      TCGA-86-8674 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-86-A456      TCGA-91-6829      TCGA-91-6830      TCGA-91-6836 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-91-6840      TCGA-91-6849      TCGA-91-8499      TCGA-91-A4BC 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043      TCGA-95-7562 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-95-7567      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP      TCGA-97-7546 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7941      TCGA-97-8171 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-97-8172      TCGA-97-8174      TCGA-97-8176      TCGA-97-8179 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7      TCGA-99-7458 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-99-8025      TCGA-99-8028      TCGA-99-8032      TCGA-J2-8194 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4T2 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8      TCGA-MP-A4T9 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE      TCGA-MP-A4TF 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" "KCTD1 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  KCTD1 MUTATED     4   1   0   0
  KCTD1 WILD-TYPE 306  10   4  25
D208V13, multiclass
    clus
vv   KCTD1 MUTATED KCTD1 WILD-TYPE
  R0             4             306
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD1 MUTATED                                  0     0
  KCTD1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCTD1 MUTATED                           0     6
  KCTD1 WILD-TYPE                        29   371
D208V14, multiclass
                                  clus
vv                                 KCTD1 MUTATED KCTD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V15, binary
                 cls
clus                0   1
  KCTD1 MUTATED     0   4
  KCTD1 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD1 MUTATED      0    4
  KCTD1 WILD-TYPE    6  345
                        clus
vv                       KCTD1 MUTATED KCTD1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(209) Variable = IRF2BP2 MUTATION ANALYSIS
D209V1, survival
                   sevent
clus2                 0   1
  IRF2BP2 MUTATED     6   1
  IRF2BP2 WILD-TYPE 309 140
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                7               449 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                1               140 
$`IRF2BP2 MUTATED`
TCGA-05-4424 TCGA-55-7574 TCGA-55-8506 TCGA-64-1681 TCGA-69-8255 TCGA-86-8669 
       30.02         3.12         0.36        38.37         4.24        30.84 
TCGA-91-6848 
        7.36 

$`IRF2BP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        20.65        55.43        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       12.56        14.01        13.45         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
        1.15        13.91        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
             0.36              0.00 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
            38.37            223.96 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
             7.36             18.08 
[1] "0.4 - 38.4 (7.4)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D209V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IRF2BP2 MUTATED         0        3        1         0         2          1
  IRF2BP2 WILD-TYPE       4      120      132        46        65         69
                   vv
clus                STAGE IIIB STAGE IV
  IRF2BP2 MUTATED            0        0
  IRF2BP2 WILD-TYPE         11       25
D209V3, multiclass
            clus
vv           IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 3               120
  STAGE IB                 1               132
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IRF2BP2 MUTATED     3   2   2   0
  IRF2BP2 WILD-TYPE 152 259  41  18
D209V4, multiclass
    clus
vv   IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  T1               3               152
  T2               2               259
  T3               2                41
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  IRF2BP2 MUTATED     6   0     1
  IRF2BP2 WILD-TYPE 301  89    71
D209V5, multiclass
       clus
vv      IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  N0                  6               301
  N1                  0                89
  N2+N3               1                71
[1] 3 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
  IRF2BP2 MUTATED     5   0
  IRF2BP2 WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      5    0
  IRF2BP2 WILD-TYPE  322   23
   clus
vv  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  0               5               322
  1               0                23
[1] 2 2
[1] FALSE
D209V7, binary
                   cls
clus                  0   1
  IRF2BP2 MUTATED     3   4
  IRF2BP2 WILD-TYPE 256 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      3    4
  IRF2BP2 WILD-TYPE  256  217
        clus
vv       IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  FEMALE               3               256
  MALE                 4               217
[1] 2 2
[1] FALSE
D209V8, continuous
[1] "Remove cluster labels:" "IRF2BP2 MUTATED"       
clus
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-5778 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8671        TCGA-86-A4JF 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  IRF2BP2 MUTATED                            0
  IRF2BP2 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  IRF2BP2 MUTATED                                   1
  IRF2BP2 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IRF2BP2 MUTATED                                                    5
  IRF2BP2 WILD-TYPE                                                289
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IRF2BP2 MUTATED                                            0
  IRF2BP2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IRF2BP2 MUTATED                                               0
  IRF2BP2 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  IRF2BP2 MUTATED                                0
  IRF2BP2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  IRF2BP2 MUTATED                                    0
  IRF2BP2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  IRF2BP2 MUTATED                              0                             0
  IRF2BP2 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IRF2BP2 MUTATED                                               1
  IRF2BP2 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  IRF2BP2 MUTATED                              0
  IRF2BP2 WILD-TYPE                            9
D209V9, multiclass
                                                    clus
vv                                                   IRF2BP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   IRF2BP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V10, binary
                   cls
clus                  0   1
  IRF2BP2 MUTATED     1   6
  IRF2BP2 WILD-TYPE  19 454
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      1    6
  IRF2BP2 WILD-TYPE   19  454
     clus
vv    IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  NO                1                19
  YES               6               454
[1] 2 2
[1] FALSE
D209V11, continuous
D209V12, continuous
                   vv
clus                 R0  R1  R2  RX
  IRF2BP2 MUTATED     3   2   0   0
  IRF2BP2 WILD-TYPE 307   9   4  25
D209V13, multiclass
    clus
vv   IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  R0               3               307
  R1               2                 9
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRF2BP2 MUTATED                                  0     0
  IRF2BP2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  IRF2BP2 MUTATED                           0     6
  IRF2BP2 WILD-TYPE                        29   371
D209V14, multiclass
                                  clus
vv                                 IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V15, binary
                   cls
clus                  0   1
  IRF2BP2 MUTATED     1   5
  IRF2BP2 WILD-TYPE   5 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      1    5
  IRF2BP2 WILD-TYPE    5  344
                        clus
vv                       IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(210) Variable = SUN1 MUTATION ANALYSIS
D210V1, survival
                sevent
clus2              0   1
  SUN1 MUTATED     9   5
  SUN1 WILD-TYPE 306 136
  SUN1 MUTATED SUN1 WILD-TYPE 
            14            442 
  SUN1 MUTATED SUN1 WILD-TYPE 
             5            136 
$`SUN1 MUTATED`
TCGA-05-4397 TCGA-38-4625 TCGA-38-4628 TCGA-38-4631 TCGA-44-A4SS TCGA-55-8092 
       24.03        97.74        49.05        11.64        13.64         5.06 
TCGA-73-4658 TCGA-73-4670 TCGA-86-8358 TCGA-91-6848 TCGA-95-7043 TCGA-99-7458 
       52.60         4.31        21.47         7.36         1.22        24.56 
TCGA-99-8025 TCGA-L9-A444 
       34.85         0.20 

$`SUN1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24         7.04         2.01         0.10        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       29.98        26.30        15.35         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8028 
       20.52        17.75        20.84        18.67        20.68        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 
       16.44        19.00        14.30         3.81        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SUN1 MUTATED SUN1 WILD-TYPE 
           0.2            0.0 
  SUN1 MUTATED SUN1 WILD-TYPE 
         97.74         223.96 
  SUN1 MUTATED SUN1 WILD-TYPE 
        17.555         18.030 
[1] "0.2 - 97.7 (17.6)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1"  
D210V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SUN1 MUTATED         0        3        5         0         3          3
  SUN1 WILD-TYPE       4      120      128        46        64         67
                vv
clus             STAGE IIIB STAGE IV
  SUN1 MUTATED            0        1
  SUN1 WILD-TYPE         11       24
D210V3, multiclass
            clus
vv           SUN1 MUTATED SUN1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              5            128
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            3             67
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SUN1 MUTATED     3   9   2   1
  SUN1 WILD-TYPE 152 252  41  17
D210V4, multiclass
    clus
vv   SUN1 MUTATED SUN1 WILD-TYPE
  T1            3            152
  T2            9            252
  T3            2             41
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  SUN1 MUTATED    11   2     2
  SUN1 WILD-TYPE 296  87    70
D210V5, multiclass
       clus
vv      SUN1 MUTATED SUN1 WILD-TYPE
  N0              11            296
  N1               2             87
  N2+N3            2             70
[1] 3 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
  SUN1 MUTATED    10   1
  SUN1 WILD-TYPE 317  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SUN1 MUTATED     10    1
  SUN1 WILD-TYPE  317   22
   clus
vv  SUN1 MUTATED SUN1 WILD-TYPE
  0           10            317
  1            1             22
[1] 2 2
[1] FALSE
D210V7, binary
                cls
clus               0   1
  SUN1 MUTATED     9   6
  SUN1 WILD-TYPE 250 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  SUN1 MUTATED      9    6
  SUN1 WILD-TYPE  250  215
        clus
vv       SUN1 MUTATED SUN1 WILD-TYPE
  FEMALE            9            250
  MALE              6            215
[1] 2 2
[1] FALSE
D210V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SUN1 MUTATED                            0                                 2
  SUN1 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SUN1 MUTATED                                                   12
  SUN1 WILD-TYPE                                                282
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SUN1 MUTATED                                            0
  SUN1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SUN1 MUTATED                                               1
  SUN1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SUN1 MUTATED                                0
  SUN1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SUN1 MUTATED                                    0
  SUN1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SUN1 MUTATED                              0                             0
  SUN1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SUN1 MUTATED                                               0
  SUN1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SUN1 MUTATED                              0
  SUN1 WILD-TYPE                            9
D210V9, multiclass
                                                    clus
vv                                                   SUN1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SUN1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V10, binary
                cls
clus               0   1
  SUN1 MUTATED     0  15
  SUN1 WILD-TYPE  20 445
[1] "tbl2"
                cls
clus             [,1] [,2]
  SUN1 MUTATED      0   15
  SUN1 WILD-TYPE   20  445
     clus
vv    SUN1 MUTATED SUN1 WILD-TYPE
  NO             0             20
  YES           15            445
[1] 2 2
[1] FALSE
D210V11, continuous
D210V12, continuous
                vv
clus              R0  R1  R2  RX
  SUN1 MUTATED    12   0   0   0
  SUN1 WILD-TYPE 298  11   4  25
D210V13, multiclass
    clus
vv   SUN1 MUTATED SUN1 WILD-TYPE
  R0           12            298
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SUN1 MUTATED                                  0     0
  SUN1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SUN1 MUTATED                           1    12
  SUN1 WILD-TYPE                        28   365
D210V14, multiclass
                                  clus
vv                                 SUN1 MUTATED SUN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      12            365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V15, binary
                cls
clus               0   1
  SUN1 MUTATED     0  13
  SUN1 WILD-TYPE   6 336
[1] "tbl2"
                cls
clus             [,1] [,2]
  SUN1 MUTATED      0   13
  SUN1 WILD-TYPE    6  336
                        clus
vv                       SUN1 MUTATED SUN1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           13            336
[1] 2 2
[1] FALSE

Clustering(211) Variable = SEMA6C MUTATION ANALYSIS
D211V1, survival
                  sevent
clus2                0   1
  SEMA6C MUTATED     2   5
  SEMA6C WILD-TYPE 313 136
  SEMA6C MUTATED SEMA6C WILD-TYPE 
               7              449 
  SEMA6C MUTATED SEMA6C WILD-TYPE 
               5              136 
$`SEMA6C MUTATED`
TCGA-05-4418 TCGA-49-4488 TCGA-50-6594 TCGA-55-8506 TCGA-78-7162 TCGA-91-6829 
        9.01        28.57        12.16         0.36       104.19        41.36 
TCGA-91-8499 
        1.18 

$`SEMA6C WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.11        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 
        5.88        64.90        22.29         7.07       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
        7.36         1.15        16.18        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  SEMA6C MUTATED SEMA6C WILD-TYPE 
            0.36             0.00 
  SEMA6C MUTATED SEMA6C WILD-TYPE 
          104.19           223.96 
  SEMA6C MUTATED SEMA6C WILD-TYPE 
           12.16            18.08 
[1] "0.4 - 104.2 (12.2)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.8"
D211V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SEMA6C MUTATED         0        3        1         0         1          2
  SEMA6C WILD-TYPE       4      120      132        46        66         68
                  vv
clus               STAGE IIIB STAGE IV
  SEMA6C MUTATED            0        0
  SEMA6C WILD-TYPE         11       25
D211V3, multiclass
            clus
vv           SEMA6C MUTATED SEMA6C WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                1              132
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SEMA6C MUTATED     3   1   3   0
  SEMA6C WILD-TYPE 152 260  40  18
D211V4, multiclass
    clus
vv   SEMA6C MUTATED SEMA6C WILD-TYPE
  T1              3              152
  T2              1              260
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  SEMA6C MUTATED     5   0     2
  SEMA6C WILD-TYPE 302  89    70
D211V5, multiclass
       clus
vv      SEMA6C MUTATED SEMA6C WILD-TYPE
  N0                 5              302
  N1                 0               89
  N2+N3              2               70
[1] 3 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
  SEMA6C MUTATED     3   0
  SEMA6C WILD-TYPE 324  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA6C MUTATED      3    0
  SEMA6C WILD-TYPE  324   23
   clus
vv  SEMA6C MUTATED SEMA6C WILD-TYPE
  0              3              324
  1              0               23
[1] 2 2
[1] FALSE
D211V7, binary
                  cls
clus                 0   1
  SEMA6C MUTATED     4   3
  SEMA6C WILD-TYPE 255 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA6C MUTATED      4    3
  SEMA6C WILD-TYPE  255  218
        clus
vv       SEMA6C MUTATED SEMA6C WILD-TYPE
  FEMALE              4              255
  MALE                3              218
[1] 2 2
[1] FALSE
D211V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SEMA6C MUTATED                            0                                 2
  SEMA6C WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SEMA6C MUTATED                                                    4
  SEMA6C WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SEMA6C MUTATED                                            0
  SEMA6C WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SEMA6C MUTATED                                               1
  SEMA6C WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SEMA6C MUTATED                                0
  SEMA6C WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SEMA6C MUTATED                                    0
  SEMA6C WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SEMA6C MUTATED                              0                             0
  SEMA6C WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SEMA6C MUTATED                                               0
  SEMA6C WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SEMA6C MUTATED                              0
  SEMA6C WILD-TYPE                            9
D211V9, multiclass
                                                    clus
vv                                                   SEMA6C MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SEMA6C WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V10, binary
                  cls
clus                 0   1
  SEMA6C MUTATED     0   7
  SEMA6C WILD-TYPE  20 453
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA6C MUTATED      0    7
  SEMA6C WILD-TYPE   20  453
     clus
vv    SEMA6C MUTATED SEMA6C WILD-TYPE
  NO               0               20
  YES              7              453
[1] 2 2
[1] FALSE
D211V11, continuous
D211V12, continuous
                  vv
clus                R0  R1  R2  RX
  SEMA6C MUTATED     5   0   0   0
  SEMA6C WILD-TYPE 305  11   4  25
D211V13, multiclass
    clus
vv   SEMA6C MUTATED SEMA6C WILD-TYPE
  R0              5              305
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEMA6C MUTATED                                  0     0
  SEMA6C WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SEMA6C MUTATED                           1     5
  SEMA6C WILD-TYPE                        28   372
D211V14, multiclass
                                  clus
vv                                 SEMA6C MUTATED SEMA6C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V15, binary
                  cls
clus                 0   1
  SEMA6C MUTATED     0   5
  SEMA6C WILD-TYPE   6 344
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA6C MUTATED      0    5
  SEMA6C WILD-TYPE    6  344
                        clus
vv                       SEMA6C MUTATED SEMA6C WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              344
[1] 2 2
[1] FALSE

Clustering(212) Variable = KLF5 MUTATION ANALYSIS
D212V1, survival
                sevent
clus2              0   1
  KLF5 MUTATED     3   0
  KLF5 WILD-TYPE 312 141
  KLF5 MUTATED KLF5 WILD-TYPE 
             3            453 
  KLF5 MUTATED KLF5 WILD-TYPE 
             0            141 
$`KLF5 MUTATED`
TCGA-44-7670 TCGA-55-7281 TCGA-78-7539 
       29.00         0.59        10.75 

$`KLF5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1.74         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        53.33        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  KLF5 MUTATED KLF5 WILD-TYPE 
          0.59           0.00 
  KLF5 MUTATED KLF5 WILD-TYPE 
         29.00         223.96 
  KLF5 MUTATED KLF5 WILD-TYPE 
         10.75          18.08 
[1] "0.6 - 29.0 (10.8)"  "0.0 - 224.0 (18.1)"
[1] "hr="     "1200000"
D212V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KLF5 MUTATED         0        1        0         2         1          0
  KLF5 WILD-TYPE       4      122      133        44        66         70
                vv
clus             STAGE IIIB STAGE IV
  KLF5 MUTATED            0        0
  KLF5 WILD-TYPE         11       25
D212V3, multiclass
            clus
vv           KLF5 MUTATED KLF5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              0            133
  STAGE IIA             2             44
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLF5 MUTATED     2   2   0   0
  KLF5 WILD-TYPE 153 259  43  18
D212V4, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  T1            2            153
  T2            2            259
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  KLF5 MUTATED     2   2     0
  KLF5 WILD-TYPE 305  87    72
D212V5, multiclass
       clus
vv      KLF5 MUTATED KLF5 WILD-TYPE
  N0               2            305
  N1               2             87
  N2+N3            0             72
[1] 3 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
  KLF5 MUTATED     4   0
  KLF5 WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      4    0
  KLF5 WILD-TYPE  323   23
   clus
vv  KLF5 MUTATED KLF5 WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D212V7, binary
                cls
clus               0   1
  KLF5 MUTATED     4   0
  KLF5 WILD-TYPE 255 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      4    0
  KLF5 WILD-TYPE  255  221
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  FEMALE            4            255
  MALE              0            221
[1] 2 2
[1] FALSE
D212V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KLF5 MUTATED                            0                                 1
  KLF5 WILD-TYPE                         18                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KLF5 MUTATED                                                    3
  KLF5 WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KLF5 MUTATED                                            0
  KLF5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KLF5 MUTATED                                               0
  KLF5 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  KLF5 MUTATED                                0
  KLF5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  KLF5 MUTATED                                    0
  KLF5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KLF5 MUTATED                              0                             0
  KLF5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KLF5 MUTATED                                               0
  KLF5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  KLF5 MUTATED                              0
  KLF5 WILD-TYPE                            9
D212V9, multiclass
                                                    clus
vv                                                   KLF5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   KLF5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V10, binary
                cls
clus               0   1
  KLF5 MUTATED     0   4
  KLF5 WILD-TYPE  20 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      0    4
  KLF5 WILD-TYPE   20  456
     clus
vv    KLF5 MUTATED KLF5 WILD-TYPE
  NO             0             20
  YES            4            456
[1] 2 2
[1] FALSE
D212V11, continuous
D212V12, continuous
                vv
clus              R0  R1  R2  RX
  KLF5 MUTATED     3   0   0   0
  KLF5 WILD-TYPE 307  11   4  25
D212V13, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  R0            3            307
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF5 MUTATED                                  0     0
  KLF5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLF5 MUTATED                           0     3
  KLF5 WILD-TYPE                        29   374
D212V14, multiclass
                                  clus
vv                                 KLF5 MUTATED KLF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       3            374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V15, binary
                cls
clus               0   1
  KLF5 MUTATED     1   0
  KLF5 WILD-TYPE   5 349
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      1    0
  KLF5 WILD-TYPE    5  349
                        clus
vv                       KLF5 MUTATED KLF5 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            0            349
[1] 2 2
[1] FALSE

Clustering(213) Variable = RFTN2 MUTATION ANALYSIS
D213V1, survival
                 sevent
clus2               0   1
  RFTN2 MUTATED     7   4
  RFTN2 WILD-TYPE 308 137
  RFTN2 MUTATED RFTN2 WILD-TYPE 
             11             445 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
              4             137 
$`RFTN2 MUTATED`
TCGA-05-4424 TCGA-49-6744 TCGA-55-1592 TCGA-55-6970 TCGA-55-A493 TCGA-55-A4DF 
       30.02        29.26        23.05        15.25         0.92        20.19 
TCGA-62-A46O TCGA-86-8073 TCGA-86-8279 TCGA-86-8585 TCGA-99-8033 
       47.80        24.33        15.85         1.15         5.59 

$`RFTN2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       29.46        29.75        55.89        14.63        12.13        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        40.73         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
        1.58        20.58        19.59        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
        4.57         0.79        15.75        16.08        15.65        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       21.47        14.60        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85        36.76         1.45        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  RFTN2 MUTATED RFTN2 WILD-TYPE 
           0.92            0.00 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
          47.80          223.96 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
          20.19           17.98 
[1] "0.9 - 47.8 (20.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.5"
D213V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RFTN2 MUTATED         0        2        4         2         1          1
  RFTN2 WILD-TYPE       4      121      129        44        66         69
                 vv
clus              STAGE IIIB STAGE IV
  RFTN2 MUTATED            0        1
  RFTN2 WILD-TYPE         11       24
D213V3, multiclass
            clus
vv           RFTN2 MUTATED RFTN2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               4             129
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RFTN2 MUTATED     1   8   1   0
  RFTN2 WILD-TYPE 154 253  42  18
D213V4, multiclass
    clus
vv   RFTN2 MUTATED RFTN2 WILD-TYPE
  T1             1             154
  T2             8             253
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  RFTN2 MUTATED     7   2     1
  RFTN2 WILD-TYPE 300  87    71
D213V5, multiclass
       clus
vv      RFTN2 MUTATED RFTN2 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             1              71
[1] 3 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
  RFTN2 MUTATED     7   1
  RFTN2 WILD-TYPE 320  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFTN2 MUTATED      7    1
  RFTN2 WILD-TYPE  320   22
   clus
vv  RFTN2 MUTATED RFTN2 WILD-TYPE
  0             7             320
  1             1              22
[1] 2 2
[1] FALSE
D213V7, binary
                 cls
clus                0   1
  RFTN2 MUTATED     5   6
  RFTN2 WILD-TYPE 254 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFTN2 MUTATED      5    6
  RFTN2 WILD-TYPE  254  215
        clus
vv       RFTN2 MUTATED RFTN2 WILD-TYPE
  FEMALE             5             254
  MALE               6             215
[1] 2 2
[1] FALSE
D213V8, continuous
[1] "Remove cluster labels:" "RFTN2 MUTATED"         
clus
  RFTN2 MUTATED RFTN2 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"RFTN2 WILD-TYPE" "RFTN2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RFTN2 MUTATED                            0                                 2
  RFTN2 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RFTN2 MUTATED                                                    6
  RFTN2 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RFTN2 MUTATED                                            0
  RFTN2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RFTN2 MUTATED                                               1
  RFTN2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RFTN2 MUTATED                                0
  RFTN2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RFTN2 MUTATED                                    0
  RFTN2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RFTN2 MUTATED                              0                             1
  RFTN2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RFTN2 MUTATED                                               1
  RFTN2 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RFTN2 MUTATED                              0
  RFTN2 WILD-TYPE                            9
D213V9, multiclass
                                                    clus
vv                                                   RFTN2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   RFTN2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V10, binary
                 cls
clus                0   1
  RFTN2 MUTATED     0  11
  RFTN2 WILD-TYPE  20 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFTN2 MUTATED      0   11
  RFTN2 WILD-TYPE   20  449
     clus
vv    RFTN2 MUTATED RFTN2 WILD-TYPE
  NO              0              20
  YES            11             449
[1] 2 2
[1] FALSE
D213V11, continuous
D213V12, continuous
                 vv
clus               R0  R1  R2  RX
  RFTN2 MUTATED     9   2   0   0
  RFTN2 WILD-TYPE 301   9   4  25
D213V13, multiclass
    clus
vv   RFTN2 MUTATED RFTN2 WILD-TYPE
  R0             9             301
  R1             2               9
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RFTN2 MUTATED                                  0     0
  RFTN2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RFTN2 MUTATED                           0    10
  RFTN2 WILD-TYPE                        29   367
D213V14, multiclass
                                  clus
vv                                 RFTN2 MUTATED RFTN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V15, binary
                 cls
clus                0   1
  RFTN2 MUTATED     0   8
  RFTN2 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFTN2 MUTATED      0    8
  RFTN2 WILD-TYPE    6  341
                        clus
vv                       RFTN2 MUTATED RFTN2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(214) Variable = ZNF81 MUTATION ANALYSIS
D214V1, survival
                 sevent
clus2               0   1
  ZNF81 MUTATED     4   3
  ZNF81 WILD-TYPE 311 138
  ZNF81 MUTATED ZNF81 WILD-TYPE 
              7             449 
  ZNF81 MUTATED ZNF81 WILD-TYPE 
              3             138 
$`ZNF81 MUTATED`
TCGA-05-4430 TCGA-38-4632 TCGA-44-7670 TCGA-55-7907 TCGA-64-5775 TCGA-73-7498 
       25.02        44.61        29.00         0.53         2.04        39.09 
TCGA-78-8662 
      110.50 

$`ZNF81 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       20.65        55.43        38.37        87.98        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        1.32         5.39         1.25        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ZNF81 MUTATED ZNF81 WILD-TYPE 
           0.53            0.00 
  ZNF81 MUTATED ZNF81 WILD-TYPE 
         110.50          223.96 
  ZNF81 MUTATED ZNF81 WILD-TYPE 
          29.00           17.92 
[1] "0.5 - 110.5 (29.0)" "0.0 - 224.0 (17.9)"
[1] "hr=" "1.3"
D214V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF81 MUTATED         0        1        2         2         0          1
  ZNF81 WILD-TYPE       4      122      131        44        67         69
                 vv
clus              STAGE IIIB STAGE IV
  ZNF81 MUTATED            0        1
  ZNF81 WILD-TYPE         11       24
D214V3, multiclass
            clus
vv           ZNF81 MUTATED ZNF81 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               2             131
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF81 MUTATED     2   4   0   1
  ZNF81 WILD-TYPE 153 257  43  17
D214V4, multiclass
    clus
vv   ZNF81 MUTATED ZNF81 WILD-TYPE
  T1             2             153
  T2             4             257
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  ZNF81 MUTATED     4   3     0
  ZNF81 WILD-TYPE 303  86    72
D214V5, multiclass
       clus
vv      ZNF81 MUTATED ZNF81 WILD-TYPE
  N0                4             303
  N1                3              86
  N2+N3             0              72
[1] 3 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
  ZNF81 MUTATED     5   1
  ZNF81 WILD-TYPE 322  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF81 MUTATED      5    1
  ZNF81 WILD-TYPE  322   22
   clus
vv  ZNF81 MUTATED ZNF81 WILD-TYPE
  0             5             322
  1             1              22
[1] 2 2
[1] FALSE
D214V7, binary
                 cls
clus                0   1
  ZNF81 MUTATED     4   3
  ZNF81 WILD-TYPE 255 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF81 MUTATED      4    3
  ZNF81 WILD-TYPE  255  218
        clus
vv       ZNF81 MUTATED ZNF81 WILD-TYPE
  FEMALE             4             255
  MALE               3             218
[1] 2 2
[1] FALSE
D214V8, continuous
[1] "Remove cluster labels:" "ZNF81 MUTATED"         
clus
  ZNF81 MUTATED ZNF81 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7499      TCGA-75-5122 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" "ZNF81 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF81 MUTATED                            0                                 1
  ZNF81 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF81 MUTATED                                                    5
  ZNF81 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF81 MUTATED                                            0
  ZNF81 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF81 MUTATED                                               1
  ZNF81 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ZNF81 MUTATED                                0
  ZNF81 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF81 MUTATED                                    0
  ZNF81 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF81 MUTATED                              0                             0
  ZNF81 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF81 MUTATED                                               0
  ZNF81 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ZNF81 MUTATED                              0
  ZNF81 WILD-TYPE                            9
D214V9, multiclass
                                                    clus
vv                                                   ZNF81 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ZNF81 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V10, binary
                 cls
clus                0   1
  ZNF81 MUTATED     0   7
  ZNF81 WILD-TYPE  20 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF81 MUTATED      0    7
  ZNF81 WILD-TYPE   20  453
     clus
vv    ZNF81 MUTATED ZNF81 WILD-TYPE
  NO              0              20
  YES             7             453
[1] 2 2
[1] FALSE
D214V11, continuous
D214V12, continuous
                 vv
clus               R0  R1  R2  RX
  ZNF81 MUTATED     6   0   0   0
  ZNF81 WILD-TYPE 304  11   4  25
D214V13, multiclass
    clus
vv   ZNF81 MUTATED ZNF81 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF81 MUTATED                                  0     0
  ZNF81 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF81 MUTATED                           1     4
  ZNF81 WILD-TYPE                        28   373
D214V14, multiclass
                                  clus
vv                                 ZNF81 MUTATED ZNF81 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V15, binary
                 cls
clus                0   1
  ZNF81 MUTATED     1   4
  ZNF81 WILD-TYPE   5 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF81 MUTATED      1    4
  ZNF81 WILD-TYPE    5  345
                        clus
vv                       ZNF81 MUTATED ZNF81 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(215) Variable = FER MUTATION ANALYSIS
D215V1, survival
               sevent
clus2             0   1
  FER MUTATED     9   3
  FER WILD-TYPE 306 138
  FER MUTATED FER WILD-TYPE 
           12           444 
  FER MUTATED FER WILD-TYPE 
            3           138 
$`FER MUTATED`
TCGA-44-4112 TCGA-49-6761 TCGA-50-5933 TCGA-55-6983 TCGA-55-7994 TCGA-55-8506 
       26.56        11.64        78.67        60.03        19.82         0.36 
TCGA-64-5775 TCGA-86-6851 TCGA-86-8358 TCGA-95-7043 TCGA-95-A4VN TCGA-MN-A4N4 
        2.04         5.88        21.47         1.22        18.18        38.63 

$`FER WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 
        5.49         7.79         2.20        45.34        32.71        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
       18.64         0.53         6.48        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       27.29         2.76        21.40        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  FER MUTATED FER WILD-TYPE 
         0.36          0.00 
  FER MUTATED FER WILD-TYPE 
        78.67        223.96 
  FER MUTATED FER WILD-TYPE 
        19.00         17.95 
[1] "0.4 - 78.7 (19.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.4"
D215V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FER MUTATED         0        2        3         2         3          2
  FER WILD-TYPE       4      121      130        44        64         68
               vv
clus            STAGE IIIB STAGE IV
  FER MUTATED            1        0
  FER WILD-TYPE         10       25
D215V3, multiclass
            clus
vv           FER MUTATED FER WILD-TYPE
  STAGE I              0             4
  STAGE IA             2           121
  STAGE IB             3           130
  STAGE IIA            2            44
  STAGE IIB            3            64
  STAGE IIIA           2            68
  STAGE IIIB           1            10
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of 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     4   4   3   2
  FER WILD-TYPE 151 257  40  16
D215V4, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  T1           4           151
  T2           4           257
  T3           3            40
  T4           2            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"
               vv
clus             N0  N1 N2+N3
  FER MUTATED     8   3     2
  FER WILD-TYPE 299  86    70
D215V5, multiclass
       clus
vv      FER MUTATED FER WILD-TYPE
  N0              8           299
  N1              3            86
  N2+N3           2            70
[1] 3 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
  FER MUTATED     9   0
  FER WILD-TYPE 318  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      9    0
  FER WILD-TYPE  318   23
   clus
vv  FER MUTATED FER WILD-TYPE
  0           9           318
  1           0            23
[1] 2 2
[1] FALSE
D215V7, binary
               cls
clus              0   1
  FER MUTATED     6   7
  FER WILD-TYPE 253 214
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      6    7
  FER WILD-TYPE  253  214
        clus
vv       FER MUTATED FER WILD-TYPE
  FEMALE           6           253
  MALE             7           214
[1] 2 2
[1] FALSE
D215V8, continuous
[1] "Remove cluster labels:" "FER MUTATED"           
clus
  FER MUTATED FER WILD-TYPE 
            2            82 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-62-A470    TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-64-5778    TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-73-4659    TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4676 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-73-7498    TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-86-7711    TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-86-8055    TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-86-8278    TCGA-86-8279    TCGA-86-8281    TCGA-86-8359    TCGA-86-8668 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-86-8669    TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458 
"FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" "FER WILD-TYPE" 
   TCGA-MN-A4N1    TCGA-MN-A4N5 
"FER WILD-TYPE" "FER WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FER MUTATED                            0                                 2
  FER WILD-TYPE                         18                               100
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FER MUTATED                                                    9
  FER WILD-TYPE                                                285
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FER MUTATED                                            0
  FER WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FER MUTATED                                               0
  FER WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  FER MUTATED                                0
  FER WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  FER MUTATED                                    0                            0
  FER WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  FER MUTATED                               0
  FER WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FER MUTATED                                               1
  FER WILD-TYPE                                             4
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  FER MUTATED                              1
  FER WILD-TYPE                            8
D215V9, multiclass
                                                    clus
vv                                                   FER MUTATED FER WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            2           100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           9           285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                1             4
  MUCINOUS (COLLOID) CARCINOMA                                 1             8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V10, binary
               cls
clus              0   1
  FER MUTATED     1  12
  FER WILD-TYPE  19 448
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      1   12
  FER WILD-TYPE   19  448
     clus
vv    FER MUTATED FER WILD-TYPE
  NO            1            19
  YES          12           448
[1] 2 2
[1] FALSE
D215V11, continuous
D215V12, continuous
               vv
clus             R0  R1  R2  RX
  FER MUTATED    10   0   0   0
  FER WILD-TYPE 300  11   4  25
D215V13, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  R0          10           300
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FER MUTATED                                  0     0
  FER WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FER MUTATED                           0    13
  FER WILD-TYPE                        29   364
D215V14, multiclass
                                  clus
vv                                 FER MUTATED FER WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                     13           364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V15, binary
               cls
clus              0   1
  FER MUTATED     0  13
  FER WILD-TYPE   6 336
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      0   13
  FER WILD-TYPE    6  336
                        clus
vv                       FER MUTATED FER WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          13           336
[1] 2 2
[1] FALSE

Clustering(216) Variable = NPHS1 MUTATION ANALYSIS
D216V1, survival
                 sevent
clus2               0   1
  NPHS1 MUTATED    16   6
  NPHS1 WILD-TYPE 299 135
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             22             434 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
              6             135 
$`NPHS1 MUTATED`
TCGA-38-4628 TCGA-44-5644 TCGA-44-7661 TCGA-44-7662 TCGA-44-8119 TCGA-50-5068 
       49.05        28.37        12.03         7.17         3.25        49.28 
TCGA-55-8207 TCGA-55-8614 TCGA-55-8616 TCGA-55-A490 TCGA-62-8399 TCGA-62-A46P 
        2.17        17.62         1.58         1.58        88.64        19.53 
TCGA-69-7765 TCGA-73-4670 TCGA-78-7155 TCGA-78-7536 TCGA-78-7542 TCGA-86-A456 
        5.42         4.31        38.50         8.02        10.55        13.32 
TCGA-91-6831 TCGA-95-7567 TCGA-97-7937 TCGA-NJ-A4YQ 
       10.19        18.67         5.95        29.13 

$`NPHS1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
      120.79        37.71        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       16.44        14.60        19.46        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
       71.47        70.55        15.72        60.16        31.04         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 
       23.64        15.65        17.98         1.08         1.51        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       19.99         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       47.80        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       13.87         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       29.98        26.30        15.35         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 
      223.96         8.48        88.14        26.53        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
       19.00        17.29         1.12         1.22         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  NPHS1 MUTATED NPHS1 WILD-TYPE 
           1.58            0.00 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
          88.64          223.96 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
          11.29           18.41 
[1] "1.6 - 88.6 (11.3)"  "0.0 - 224.0 (18.4)"
[1] "hr=" "1"  
D216V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NPHS1 MUTATED         0        2       11         1         5          3
  NPHS1 WILD-TYPE       4      121      122        45        62         67
                 vv
clus              STAGE IIIB STAGE IV
  NPHS1 MUTATED            0        2
  NPHS1 WILD-TYPE         11       23
D216V3, multiclass
            clus
vv           NPHS1 MUTATED NPHS1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB              11             122
  STAGE IIA              1              45
  STAGE IIB              5              62
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of 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     2  20   1   1
  NPHS1 WILD-TYPE 153 241  42  17
D216V4, multiclass
    clus
vv   NPHS1 MUTATED NPHS1 WILD-TYPE
  T1             2             153
  T2            20             241
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  NPHS1 MUTATED    17   4     3
  NPHS1 WILD-TYPE 290  85    69
D216V5, multiclass
       clus
vv      NPHS1 MUTATED NPHS1 WILD-TYPE
  N0               17             290
  N1                4              85
  N2+N3             3              69
[1] 3 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
  NPHS1 MUTATED    14   1
  NPHS1 WILD-TYPE 313  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED     14    1
  NPHS1 WILD-TYPE  313   22
   clus
vv  NPHS1 MUTATED NPHS1 WILD-TYPE
  0            14             313
  1             1              22
[1] 2 2
[1] FALSE
D216V7, binary
                 cls
clus                0   1
  NPHS1 MUTATED    10  14
  NPHS1 WILD-TYPE 249 207
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED     10   14
  NPHS1 WILD-TYPE  249  207
        clus
vv       NPHS1 MUTATED NPHS1 WILD-TYPE
  FEMALE            10             249
  MALE              14             207
[1] 2 2
[1] FALSE
D216V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NPHS1 MUTATED                            1                                 3
  NPHS1 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NPHS1 MUTATED                                                   17
  NPHS1 WILD-TYPE                                                277
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NPHS1 MUTATED                                            0
  NPHS1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NPHS1 MUTATED                                               0
  NPHS1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NPHS1 MUTATED                                0
  NPHS1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NPHS1 MUTATED                                    1
  NPHS1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NPHS1 MUTATED                              0                             2
  NPHS1 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NPHS1 MUTATED                                               0
  NPHS1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NPHS1 MUTATED                              0
  NPHS1 WILD-TYPE                            9
D216V9, multiclass
                                                    clus
vv                                                   NPHS1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NPHS1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V10, binary
                 cls
clus                0   1
  NPHS1 MUTATED     1  23
  NPHS1 WILD-TYPE  19 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED      1   23
  NPHS1 WILD-TYPE   19  437
     clus
vv    NPHS1 MUTATED NPHS1 WILD-TYPE
  NO              1              19
  YES            23             437
[1] 2 2
[1] FALSE
D216V11, continuous
D216V12, continuous
                 vv
clus               R0  R1  R2  RX
  NPHS1 MUTATED    14   0   0   1
  NPHS1 WILD-TYPE 296  11   4  24
D216V13, multiclass
    clus
vv   NPHS1 MUTATED NPHS1 WILD-TYPE
  R0            14             296
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NPHS1 MUTATED                                  0     1
  NPHS1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NPHS1 MUTATED                           1    20
  NPHS1 WILD-TYPE                        28   357
D216V14, multiclass
                                  clus
vv                                 NPHS1 MUTATED NPHS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       20             357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V15, binary
                 cls
clus                0   1
  NPHS1 MUTATED     0  19
  NPHS1 WILD-TYPE   6 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED      0   19
  NPHS1 WILD-TYPE    6  330
                        clus
vv                       NPHS1 MUTATED NPHS1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            19             330
[1] 2 2
[1] FALSE

Clustering(217) Variable = KDR MUTATION ANALYSIS
D217V1, survival
               sevent
clus2             0   1
  KDR MUTATED    32  10
  KDR WILD-TYPE 283 131
  KDR MUTATED KDR WILD-TYPE 
           42           414 
  KDR MUTATED KDR WILD-TYPE 
           10           131 
$`KDR MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4424 TCGA-05-4430 TCGA-38-4626 TCGA-38-4631 
       19.96        14.01        30.02        25.02       120.79        11.64 
TCGA-44-4112 TCGA-44-6776 TCGA-44-A4SS TCGA-44-A4SU TCGA-50-5049 TCGA-50-5066 
       26.56        63.72        13.64        13.45        70.55        31.04 
TCGA-50-6590 TCGA-50-6594 TCGA-55-6985 TCGA-55-7227 TCGA-55-7281 TCGA-55-7994 
       42.35        12.16        40.54         1.74         0.59        19.82 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8620 TCGA-55-A494 TCGA-62-A46O TCGA-64-5775 
        0.13        17.98         2.17        15.81        47.80         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-67-3773 TCGA-69-7763 TCGA-69-7979 TCGA-73-4666 
       42.90        51.25        14.04        22.68         2.93        26.30 
TCGA-73-4668 TCGA-78-7166 TCGA-78-8662 TCGA-86-8279 TCGA-86-8358 TCGA-91-6848 
       15.35         8.48       110.50        15.85        21.47         7.36 
TCGA-95-7039 TCGA-95-7562 TCGA-97-A4LX TCGA-97-A4M0 TCGA-L9-A444 TCGA-NJ-A4YQ 
        1.12         2.86        20.19        21.44         0.20        29.13 

$`KDR WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        29.98        12.00        21.99        26.01 
TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        8.68        97.74        37.71        49.05        28.41        35.28 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
       20.52        71.47        15.72        60.16        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       15.12        18.64        29.03        25.12        22.55         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
       60.03        24.99       107.21        70.26         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 
       15.19         3.29        19.66        19.73         5.06        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59         0.92        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       55.43        38.37        87.98        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       18.84         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.30        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       52.60        23.38        29.98         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        7.07       104.19       223.96        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      214.62        39.75        77.59        10.55        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 
        0.79        15.75        16.08        15.65        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
        1.08        19.00        17.29         1.22        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  KDR MUTATED KDR WILD-TYPE 
         0.13          0.00 
  KDR MUTATED KDR WILD-TYPE 
       120.79        223.96 
  KDR MUTATED KDR WILD-TYPE 
         18.9          18.0 
[1] "0.1 - 120.8 (18.9)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.5"
D217V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KDR MUTATED         0        8       18         3         5          5
  KDR WILD-TYPE       4      115      115        43        62         65
               vv
clus            STAGE IIIB STAGE IV
  KDR MUTATED            0        3
  KDR WILD-TYPE         11       22
D217V3, multiclass
            clus
vv           KDR MUTATED KDR WILD-TYPE
  STAGE I              0             4
  STAGE IA             8           115
  STAGE IB            18           115
  STAGE IIA            3            43
  STAGE IIB            5            62
  STAGE IIIA           5            65
  STAGE IIIB           0            11
  STAGE IV             3            22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  KDR MUTATED    10  26   5   1
  KDR WILD-TYPE 145 235  38  17
D217V4, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  T1          10           145
  T2          26           235
  T3           5            38
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  KDR MUTATED    33   6     3
  KDR WILD-TYPE 274  83    69
D217V5, multiclass
       clus
vv      KDR MUTATED KDR WILD-TYPE
  N0             33           274
  N1              6            83
  N2+N3           3            69
[1] 3 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
  KDR MUTATED    28   3
  KDR WILD-TYPE 299  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     28    3
  KDR WILD-TYPE  299   20
   clus
vv  KDR MUTATED KDR WILD-TYPE
  0          28           299
  1           3            20
[1] 2 2
[1] FALSE
D217V7, binary
               cls
clus              0   1
  KDR MUTATED    23  19
  KDR WILD-TYPE 236 202
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     23   19
  KDR WILD-TYPE  236  202
        clus
vv       KDR MUTATED KDR WILD-TYPE
  FEMALE          23           236
  MALE            19           202
[1] 2 2
[1] FALSE
D217V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KDR MUTATED                            1                                10
  KDR WILD-TYPE                         17                                92
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KDR MUTATED                                                   29
  KDR WILD-TYPE                                                265
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KDR MUTATED                                            0
  KDR WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KDR MUTATED                                               1
  KDR WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  KDR MUTATED                                0
  KDR WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  KDR MUTATED                                    1                            0
  KDR WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  KDR MUTATED                               0
  KDR WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KDR MUTATED                                               0
  KDR WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  KDR MUTATED                              0
  KDR WILD-TYPE                            9
D217V9, multiclass
                                                    clus
vv                                                   KDR MUTATED KDR WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           10            92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          29           265
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           1             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V10, binary
               cls
clus              0   1
  KDR MUTATED     3  39
  KDR WILD-TYPE  17 421
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      3   39
  KDR WILD-TYPE   17  421
     clus
vv    KDR MUTATED KDR WILD-TYPE
  NO            3            17
  YES          39           421
[1] 2 2
[1] FALSE
D217V11, continuous
D217V12, continuous
               vv
clus             R0  R1  R2  RX
  KDR MUTATED    26   1   0   3
  KDR WILD-TYPE 284  10   4  22
D217V13, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  R0          26           284
  R1           1            10
  R2           0             4
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDR MUTATED                                  1     0
  KDR WILD-TYPE                                0     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  KDR MUTATED                           3    33
  KDR WILD-TYPE                        26   344
D217V14, multiclass
                                  clus
vv                                 KDR MUTATED KDR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  3            26
  WHITE                                     33           344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V15, binary
               cls
clus              0   1
  KDR MUTATED     0  33
  KDR WILD-TYPE   6 316
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      0   33
  KDR WILD-TYPE    6  316
                        clus
vv                       KDR MUTATED KDR WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          33           316
[1] 2 2
[1] FALSE

Clustering(218) Variable = LDB2 MUTATION ANALYSIS
D218V1, survival
                sevent
clus2              0   1
  LDB2 MUTATED    12   7
  LDB2 WILD-TYPE 303 134
  LDB2 MUTATED LDB2 WILD-TYPE 
            19            437 
  LDB2 MUTATED LDB2 WILD-TYPE 
             7            134 
$`LDB2 MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4417 TCGA-05-4427 TCGA-38-4628 TCGA-44-8120 
       19.96        37.02        14.96        26.01        49.05         8.55 
TCGA-50-5935 TCGA-50-6590 TCGA-55-8085 TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 
       21.47        42.35        29.72        15.42         0.36         0.26 
TCGA-62-8399 TCGA-62-A46P TCGA-64-1679 TCGA-91-6829 TCGA-95-8039 TCGA-97-A4M7 
       88.64        19.53        55.43        41.36        27.29        20.68 
TCGA-J2-A4AD 
       18.08 

$`LDB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
        8.68        97.74       120.79        37.71        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        9.27        14.27        40.60        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15        19.82         0.16        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        22.16         1.45         0.76 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
       39.98        42.38        14.60        49.25        47.80        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        20.65        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       20.52        17.75        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
       36.76         1.45         5.59        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  LDB2 MUTATED LDB2 WILD-TYPE 
          0.26           0.00 
  LDB2 MUTATED LDB2 WILD-TYPE 
         88.64         223.96 
  LDB2 MUTATED LDB2 WILD-TYPE 
         21.47          17.65 
[1] "0.3 - 88.6 (21.5)"  "0.0 - 224.0 (17.6)"
[1] "hr=" "1.1"
D218V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LDB2 MUTATED         0        7        7         0         3          2
  LDB2 WILD-TYPE       4      116      126        46        64         68
                vv
clus             STAGE IIIB STAGE IV
  LDB2 MUTATED            0        0
  LDB2 WILD-TYPE         11       25
D218V3, multiclass
            clus
vv           LDB2 MUTATED LDB2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              7            116
  STAGE IB              7            126
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LDB2 MUTATED     8  10   1   0
  LDB2 WILD-TYPE 147 251  42  18
D218V4, multiclass
    clus
vv   LDB2 MUTATED LDB2 WILD-TYPE
  T1            8            147
  T2           10            251
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  LDB2 MUTATED    15   2     2
  LDB2 WILD-TYPE 292  87    70
D218V5, multiclass
       clus
vv      LDB2 MUTATED LDB2 WILD-TYPE
  N0              15            292
  N1               2             87
  N2+N3            2             70
[1] 3 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
  LDB2 MUTATED    13   0
  LDB2 WILD-TYPE 314  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDB2 MUTATED     13    0
  LDB2 WILD-TYPE  314   23
   clus
vv  LDB2 MUTATED LDB2 WILD-TYPE
  0           13            314
  1            0             23
[1] 2 2
[1] FALSE
D218V7, binary
                cls
clus               0   1
  LDB2 MUTATED    10   9
  LDB2 WILD-TYPE 249 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDB2 MUTATED     10    9
  LDB2 WILD-TYPE  249  212
        clus
vv       LDB2 MUTATED LDB2 WILD-TYPE
  FEMALE           10            249
  MALE              9            212
[1] 2 2
[1] FALSE
D218V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LDB2 MUTATED                            1                                 6
  LDB2 WILD-TYPE                         17                                96
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LDB2 MUTATED                                                    9
  LDB2 WILD-TYPE                                                285
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LDB2 MUTATED                                            0
  LDB2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LDB2 MUTATED                                               1
  LDB2 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  LDB2 MUTATED                                0
  LDB2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  LDB2 MUTATED                                    0
  LDB2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LDB2 MUTATED                              0                             2
  LDB2 WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LDB2 MUTATED                                               0
  LDB2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  LDB2 MUTATED                              0
  LDB2 WILD-TYPE                            9
D218V9, multiclass
                                                    clus
vv                                                   LDB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   LDB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V10, binary
                cls
clus               0   1
  LDB2 MUTATED     1  18
  LDB2 WILD-TYPE  19 442
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDB2 MUTATED      1   18
  LDB2 WILD-TYPE   19  442
     clus
vv    LDB2 MUTATED LDB2 WILD-TYPE
  NO             1             19
  YES           18            442
[1] 2 2
[1] FALSE
D218V11, continuous
D218V12, continuous
                vv
clus              R0  R1  R2  RX
  LDB2 MUTATED    14   0   0   2
  LDB2 WILD-TYPE 296  11   4  23
D218V13, multiclass
    clus
vv   LDB2 MUTATED LDB2 WILD-TYPE
  R0           14            296
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LDB2 MUTATED                                  0     0
  LDB2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LDB2 MUTATED                           1    14
  LDB2 WILD-TYPE                        28   363
D218V14, multiclass
                                  clus
vv                                 LDB2 MUTATED LDB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      14            363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V15, binary
                cls
clus               0   1
  LDB2 MUTATED     0  15
  LDB2 WILD-TYPE   6 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDB2 MUTATED      0   15
  LDB2 WILD-TYPE    6  334
                        clus
vv                       LDB2 MUTATED LDB2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           15            334
[1] 2 2
[1] FALSE

Clustering(219) Variable = FIBP MUTATION ANALYSIS
D219V1, survival
                sevent
clus2              0   1
  FIBP MUTATED     5   0
  FIBP WILD-TYPE 310 141
  FIBP MUTATED FIBP WILD-TYPE 
             5            451 
  FIBP MUTATED FIBP WILD-TYPE 
             0            141 
$`FIBP MUTATED`
TCGA-44-8117 TCGA-55-7994 TCGA-69-7764 TCGA-73-4676 TCGA-78-7539 
       12.66        19.82        13.61         5.39        10.75 

$`FIBP WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         1.32         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  FIBP MUTATED FIBP WILD-TYPE 
          5.39           0.00 
  FIBP MUTATED FIBP WILD-TYPE 
         19.82         223.96 
  FIBP MUTATED FIBP WILD-TYPE 
         12.66          18.12 
[1] "5.4 - 19.8 (12.7)"  "0.0 - 224.0 (18.1)"
[1] "hr="     "3300000"
D219V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FIBP MUTATED         0        1        1         2         1          0
  FIBP WILD-TYPE       4      122      132        44        66         70
                vv
clus             STAGE IIIB STAGE IV
  FIBP MUTATED            0        0
  FIBP WILD-TYPE         11       25
D219V3, multiclass
            clus
vv           FIBP MUTATED FIBP WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              1            132
  STAGE IIA             2             44
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of 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     1   3   1   0
  FIBP WILD-TYPE 154 258  42  18
D219V4, multiclass
    clus
vv   FIBP MUTATED FIBP WILD-TYPE
  T1            1            154
  T2            3            258
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  FIBP MUTATED     4   1     0
  FIBP WILD-TYPE 303  88    72
D219V5, multiclass
       clus
vv      FIBP MUTATED FIBP WILD-TYPE
  N0               4            303
  N1               1             88
  N2+N3            0             72
[1] 3 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
  FIBP MUTATED     4   0
  FIBP WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED      4    0
  FIBP WILD-TYPE  323   23
   clus
vv  FIBP MUTATED FIBP WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D219V7, binary
                cls
clus               0   1
  FIBP MUTATED     2   3
  FIBP WILD-TYPE 257 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED      2    3
  FIBP WILD-TYPE  257  218
        clus
vv       FIBP MUTATED FIBP WILD-TYPE
  FEMALE            2            257
  MALE              3            218
[1] 2 2
[1] FALSE
D219V8, continuous
[1] "Remove cluster labels:" "FIBP MUTATED"          
clus
  FIBP MUTATED FIBP WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-73-4668     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"FIBP WILD-TYPE" "FIBP WILD-TYPE" "FIBP WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FIBP MUTATED                            0                                 2
  FIBP WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FIBP MUTATED                                                    3
  FIBP WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FIBP MUTATED                                            0
  FIBP WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FIBP MUTATED                                               0
  FIBP WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  FIBP MUTATED                                0
  FIBP WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  FIBP MUTATED                                    0
  FIBP WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FIBP MUTATED                              0                             0
  FIBP WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FIBP MUTATED                                               0
  FIBP WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  FIBP MUTATED                              0
  FIBP WILD-TYPE                            9
D219V9, multiclass
                                                    clus
vv                                                   FIBP MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   FIBP WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V10, binary
                cls
clus               0   1
  FIBP MUTATED     1   4
  FIBP WILD-TYPE  19 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED      1    4
  FIBP WILD-TYPE   19  456
     clus
vv    FIBP MUTATED FIBP WILD-TYPE
  NO             1             19
  YES            4            456
[1] 2 2
[1] FALSE
D219V11, continuous
D219V12, continuous
                vv
clus              R0  R1  R2  RX
  FIBP MUTATED     3   0   0   0
  FIBP WILD-TYPE 307  11   4  25
D219V13, multiclass
    clus
vv   FIBP MUTATED FIBP WILD-TYPE
  R0            3            307
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FIBP MUTATED                                  0     0
  FIBP WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FIBP MUTATED                           0     5
  FIBP WILD-TYPE                        29   372
D219V14, multiclass
                                  clus
vv                                 FIBP MUTATED FIBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V15, binary
                cls
clus               0   1
  FIBP MUTATED     0   4
  FIBP WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED      0    4
  FIBP WILD-TYPE    6  345
                        clus
vv                       FIBP MUTATED FIBP WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(220) Variable = MSH2 MUTATION ANALYSIS
D220V1, survival
                sevent
clus2              0   1
  MSH2 MUTATED     8   1
  MSH2 WILD-TYPE 307 140
  MSH2 MUTATED MSH2 WILD-TYPE 
             9            447 
  MSH2 MUTATED MSH2 WILD-TYPE 
             1            140 
$`MSH2 MUTATED`
TCGA-05-4417 TCGA-05-4427 TCGA-50-5931 TCGA-69-8255 TCGA-73-4668 TCGA-86-8585 
       14.96        26.01        14.27         4.24        15.35         1.15 
TCGA-86-A4JF TCGA-97-A4M0 TCGA-NJ-A4YQ 
       17.62        21.44        29.13 

$`MSH2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.22         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 
        2.93        12.56        14.01        13.45         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        0.10        52.60        23.38        29.98        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.58        20.19        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13         1.64         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MSH2 MUTATED MSH2 WILD-TYPE 
          1.15           0.00 
  MSH2 MUTATED MSH2 WILD-TYPE 
         29.13         223.96 
  MSH2 MUTATED MSH2 WILD-TYPE 
         15.35          18.12 
[1] "1.1 - 29.1 (15.3)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D220V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MSH2 MUTATED         0        2        5         0         3          1
  MSH2 WILD-TYPE       4      121      128        46        64         69
                vv
clus             STAGE IIIB STAGE IV
  MSH2 MUTATED            0        0
  MSH2 WILD-TYPE         11       25
D220V3, multiclass
            clus
vv           MSH2 MUTATED MSH2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              5            128
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH2 MUTATED     2   7   2   0
  MSH2 WILD-TYPE 153 254  41  18
D220V4, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  T1            2            153
  T2            7            254
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  MSH2 MUTATED     8   2     1
  MSH2 WILD-TYPE 299  87    71
D220V5, multiclass
       clus
vv      MSH2 MUTATED MSH2 WILD-TYPE
  N0               8            299
  N1               2             87
  N2+N3            1             71
[1] 3 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
  MSH2 MUTATED    10   0
  MSH2 WILD-TYPE 317  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     10    0
  MSH2 WILD-TYPE  317   23
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0           10            317
  1            0             23
[1] 2 2
[1] FALSE
D220V7, binary
                cls
clus               0   1
  MSH2 MUTATED     8   3
  MSH2 WILD-TYPE 251 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      8    3
  MSH2 WILD-TYPE  251  218
        clus
vv       MSH2 MUTATED MSH2 WILD-TYPE
  FEMALE            8            251
  MALE              3            218
[1] 2 2
[1] FALSE
D220V8, continuous
[1] "Remove cluster labels:" "MSH2 MUTATED"          
clus
  MSH2 MUTATED MSH2 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MSH2 MUTATED                            0                                 3
  MSH2 WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MSH2 MUTATED                                                    4
  MSH2 WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MSH2 MUTATED                                            0
  MSH2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MSH2 MUTATED                                               0
  MSH2 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MSH2 MUTATED                                0
  MSH2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MSH2 MUTATED                                    1
  MSH2 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MSH2 MUTATED                              0                             1
  MSH2 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MSH2 MUTATED                                               2
  MSH2 WILD-TYPE                                             3
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MSH2 MUTATED                              0
  MSH2 WILD-TYPE                            9
D220V9, multiclass
                                                    clus
vv                                                   MSH2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 2
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MSH2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   3
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V10, binary
                cls
clus               0   1
  MSH2 MUTATED     0  11
  MSH2 WILD-TYPE  20 449
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      0   11
  MSH2 WILD-TYPE   20  449
     clus
vv    MSH2 MUTATED MSH2 WILD-TYPE
  NO             0             20
  YES           11            449
[1] 2 2
[1] FALSE
D220V11, continuous
D220V12, continuous
                vv
clus              R0  R1  R2  RX
  MSH2 MUTATED     7   0   1   1
  MSH2 WILD-TYPE 303  11   3  24
D220V13, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  R0            7            303
  R1            0             11
  R2            1              3
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH2 MUTATED                                  1     0
  MSH2 WILD-TYPE                                0     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH2 MUTATED                           0     7
  MSH2 WILD-TYPE                        29   370
D220V14, multiclass
                                  clus
vv                                 MSH2 MUTATED MSH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V15, binary
                cls
clus               0   1
  MSH2 MUTATED     1   7
  MSH2 WILD-TYPE   5 342
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      1    7
  MSH2 WILD-TYPE    5  342
                        clus
vv                       MSH2 MUTATED MSH2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            7            342
[1] 2 2
[1] FALSE

Clustering(221) Variable = PARD3B MUTATION ANALYSIS
D221V1, survival
                  sevent
clus2                0   1
  PARD3B MUTATED    17  10
  PARD3B WILD-TYPE 298 131
  PARD3B MUTATED PARD3B WILD-TYPE 
              27              429 
  PARD3B MUTATED PARD3B WILD-TYPE 
              10              131 
$`PARD3B MUTATED`
TCGA-05-4427 TCGA-44-7672 TCGA-49-4486 TCGA-49-4488 TCGA-49-6742 TCGA-50-5049 
       26.01        23.64        76.21        28.57        14.63        70.55 
TCGA-50-6592 TCGA-50-6593 TCGA-53-7624 TCGA-55-1595 TCGA-55-8207 TCGA-55-8506 
       25.55        11.05        34.29        48.62         2.17         0.36 
TCGA-64-5781 TCGA-69-7973 TCGA-73-4666 TCGA-73-4677 TCGA-78-7153 TCGA-78-7160 
       51.25         7.56        26.30         1.25        24.99        22.29 
TCGA-86-8073 TCGA-86-8358 TCGA-91-A4BC TCGA-95-7043 TCGA-97-7938 TCGA-MP-A4T4 
       24.33        21.47         1.45         1.22         0.59        86.04 
TCGA-MP-A4TF TCGA-NJ-A4YF TCGA-NJ-A4YI 
       11.05        71.05         0.13 

$`PARD3B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        29.00        17.59        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.64        13.45        28.11        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
        3.91        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       23.05         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       38.37        87.98         2.04        42.90        28.41        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
        6.64         6.12        22.68        13.61         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         1.32         5.39        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       64.90         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.18        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
       64.60        63.52        43.79        25.48         5.95         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23         2.43        10.09        29.46        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       19.13        73.91        62.60         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  PARD3B MUTATED PARD3B WILD-TYPE 
            0.13             0.00 
  PARD3B MUTATED PARD3B WILD-TYPE 
           86.04           223.96 
  PARD3B MUTATED PARD3B WILD-TYPE 
           23.64            17.75 
[1] "0.1 - 86.0 (23.6)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1"  
D221V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PARD3B MUTATED         0        9        7         2         4          2
  PARD3B WILD-TYPE       4      114      126        44        63         68
                  vv
clus               STAGE IIIB STAGE IV
  PARD3B MUTATED            0        3
  PARD3B WILD-TYPE         11       22
D221V3, multiclass
            clus
vv           PARD3B MUTATED PARD3B WILD-TYPE
  STAGE I                 0                4
  STAGE IA                9              114
  STAGE IB                7              126
  STAGE IIA               2               44
  STAGE IIB               4               63
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                3               22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PARD3B MUTATED     9  16   1   1
  PARD3B WILD-TYPE 146 245  42  17
D221V4, multiclass
    clus
vv   PARD3B MUTATED PARD3B WILD-TYPE
  T1              9              146
  T2             16              245
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  PARD3B MUTATED    21   3     3
  PARD3B WILD-TYPE 286  86    69
D221V5, multiclass
       clus
vv      PARD3B MUTATED PARD3B WILD-TYPE
  N0                21              286
  N1                 3               86
  N2+N3              3               69
[1] 3 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
  PARD3B MUTATED    18   3
  PARD3B WILD-TYPE 309  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD3B MUTATED     18    3
  PARD3B WILD-TYPE  309   20
   clus
vv  PARD3B MUTATED PARD3B WILD-TYPE
  0             18              309
  1              3               20
[1] 2 2
[1] FALSE
D221V7, binary
                  cls
clus                 0   1
  PARD3B MUTATED    18   9
  PARD3B WILD-TYPE 241 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD3B MUTATED     18    9
  PARD3B WILD-TYPE  241  212
        clus
vv       PARD3B MUTATED PARD3B WILD-TYPE
  FEMALE             18              241
  MALE                9              212
[1] 2 2
[1] FALSE
D221V8, continuous
[1] "Remove cluster labels:" "PARD3B MUTATED"        
clus
  PARD3B MUTATED PARD3B WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4668 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8359 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"PARD3B WILD-TYPE" "PARD3B WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PARD3B MUTATED                            1                                 8
  PARD3B WILD-TYPE                         17                                94
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PARD3B MUTATED                                                   13
  PARD3B WILD-TYPE                                                281
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PARD3B MUTATED                                            0
  PARD3B WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PARD3B MUTATED                                               2
  PARD3B WILD-TYPE                                            17
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  PARD3B MUTATED                                1
  PARD3B WILD-TYPE                              1
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  PARD3B MUTATED                                    0
  PARD3B WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PARD3B MUTATED                              0                             1
  PARD3B WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PARD3B MUTATED                                               0
  PARD3B WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  PARD3B MUTATED                              1
  PARD3B WILD-TYPE                            8
D221V9, multiclass
                                                    clus
vv                                                   PARD3B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    1
                                                    clus
vv                                                   PARD3B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    17
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V10, binary
                  cls
clus                 0   1
  PARD3B MUTATED     2  25
  PARD3B WILD-TYPE  18 435
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD3B MUTATED      2   25
  PARD3B WILD-TYPE   18  435
     clus
vv    PARD3B MUTATED PARD3B WILD-TYPE
  NO               2               18
  YES             25              435
[1] 2 2
[1] FALSE
D221V11, continuous
D221V12, continuous
                  vv
clus                R0  R1  R2  RX
  PARD3B MUTATED    18   0   0   0
  PARD3B WILD-TYPE 292  11   4  25
D221V13, multiclass
    clus
vv   PARD3B MUTATED PARD3B WILD-TYPE
  R0             18              292
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARD3B MUTATED                                  0     1
  PARD3B WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PARD3B MUTATED                           1    24
  PARD3B WILD-TYPE                        28   353
D221V14, multiclass
                                  clus
vv                                 PARD3B MUTATED PARD3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        24              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V15, binary
                  cls
clus                 0   1
  PARD3B MUTATED     1  21
  PARD3B WILD-TYPE   5 328
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD3B MUTATED      1   21
  PARD3B WILD-TYPE    5  328
                        clus
vv                       PARD3B MUTATED PARD3B WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             21              328
[1] 2 2
[1] FALSE

Clustering(222) Variable = LARS MUTATION ANALYSIS
D222V1, survival
                sevent
clus2              0   1
  LARS MUTATED     2   4
  LARS WILD-TYPE 313 137
  LARS MUTATED LARS WILD-TYPE 
             6            450 
  LARS MUTATED LARS WILD-TYPE 
             4            137 
$`LARS MUTATED`
TCGA-05-4382 TCGA-50-5930 TCGA-50-5931 TCGA-67-3771 TCGA-78-7220 TCGA-78-7536 
       19.96         9.27        14.27        20.05        26.53         8.02 

$`LARS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 
       15.72        60.16        31.04        49.28         8.22        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        8.48        88.14        31.20        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  LARS MUTATED LARS WILD-TYPE 
          8.02           0.00 
  LARS MUTATED LARS WILD-TYPE 
         26.53         223.96 
  LARS MUTATED LARS WILD-TYPE 
        17.115         18.030 
[1] "8.0 - 26.5 (17.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "3.9"
D222V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LARS MUTATED         0        1        2         0         0          4
  LARS WILD-TYPE       4      122      131        46        67         66
                vv
clus             STAGE IIIB STAGE IV
  LARS MUTATED            0        0
  LARS WILD-TYPE         11       25
D222V3, multiclass
            clus
vv           LARS MUTATED LARS WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            131
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            4             66
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LARS MUTATED     1   6   0   0
  LARS WILD-TYPE 154 255  43  18
D222V4, multiclass
    clus
vv   LARS MUTATED LARS WILD-TYPE
  T1            1            154
  T2            6            255
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  LARS MUTATED     3   0     4
  LARS WILD-TYPE 304  89    68
D222V5, multiclass
       clus
vv      LARS MUTATED LARS WILD-TYPE
  N0               3            304
  N1               0             89
  N2+N3            4             68
[1] 3 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
  LARS MUTATED     7   0
  LARS WILD-TYPE 320  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  LARS MUTATED      7    0
  LARS WILD-TYPE  320   23
   clus
vv  LARS MUTATED LARS WILD-TYPE
  0            7            320
  1            0             23
[1] 2 2
[1] FALSE
D222V7, binary
                cls
clus               0   1
  LARS MUTATED     4   3
  LARS WILD-TYPE 255 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  LARS MUTATED      4    3
  LARS WILD-TYPE  255  218
        clus
vv       LARS MUTATED LARS WILD-TYPE
  FEMALE            4            255
  MALE              3            218
[1] 2 2
[1] FALSE
D222V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LARS MUTATED                            0                                 3
  LARS WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LARS MUTATED                                                    4
  LARS WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LARS MUTATED                                            0
  LARS WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LARS MUTATED                                               0
  LARS WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  LARS MUTATED                                0
  LARS WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  LARS MUTATED                                    0
  LARS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LARS MUTATED                              0                             0
  LARS WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LARS MUTATED                                               0
  LARS WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  LARS MUTATED                              0
  LARS WILD-TYPE                            9
D222V9, multiclass
                                                    clus
vv                                                   LARS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   LARS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V10, binary
                cls
clus               0   1
  LARS MUTATED     3   4
  LARS WILD-TYPE  17 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  LARS MUTATED      3    4
  LARS WILD-TYPE   17  456
     clus
vv    LARS MUTATED LARS WILD-TYPE
  NO             3             17
  YES            4            456
[1] 2 2
[1] FALSE
D222V11, continuous
D222V12, continuous
                vv
clus              R0  R1  R2  RX
  LARS MUTATED     6   0   0   0
  LARS WILD-TYPE 304  11   4  25
D222V13, multiclass
    clus
vv   LARS MUTATED LARS WILD-TYPE
  R0            6            304
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LARS MUTATED                                  0     0
  LARS WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LARS MUTATED                           1     4
  LARS WILD-TYPE                        28   373
D222V14, multiclass
                                  clus
vv                                 LARS MUTATED LARS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       4            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V15, binary
                cls
clus               0   1
  LARS MUTATED     0   3
  LARS WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  LARS MUTATED      0    3
  LARS WILD-TYPE    6  346
                        clus
vv                       LARS MUTATED LARS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(223) Variable = LCE2B MUTATION ANALYSIS
D223V1, survival
                 sevent
clus2               0   1
  LCE2B MUTATED     5   3
  LCE2B WILD-TYPE 310 138
  LCE2B MUTATED LCE2B WILD-TYPE 
              8             448 
  LCE2B MUTATED LCE2B WILD-TYPE 
              3             138 
$`LCE2B MUTATED`
TCGA-05-4382 TCGA-50-5933 TCGA-69-7973 TCGA-78-7148 TCGA-78-8640 TCGA-78-8662 
       19.96        78.67         7.56        20.58       214.62       110.50 
TCGA-86-8279 TCGA-MN-A4N4 
       15.85        38.63 

$`LCE2B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         5.42         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
       23.51       163.10        27.16         5.69        19.27        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        10.55        32.68        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.65        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  LCE2B MUTATED LCE2B WILD-TYPE 
           7.56            0.00 
  LCE2B MUTATED LCE2B WILD-TYPE 
         214.62          223.96 
  LCE2B MUTATED LCE2B WILD-TYPE 
         29.605          17.835 
[1] "7.6 - 214.6 (29.6)" "0.0 - 224.0 (17.8)"
[1] "hr=" "2.4"
D223V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LCE2B MUTATED         0        1        3         2         1          0
  LCE2B WILD-TYPE       4      122      130        44        66         70
                 vv
clus              STAGE IIIB STAGE IV
  LCE2B MUTATED            1        0
  LCE2B WILD-TYPE         10       25
D223V3, multiclass
            clus
vv           LCE2B MUTATED LCE2B WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LCE2B MUTATED     2   5   0   1
  LCE2B WILD-TYPE 153 256  43  17
D223V4, multiclass
    clus
vv   LCE2B MUTATED LCE2B WILD-TYPE
  T1             2             153
  T2             5             256
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  LCE2B MUTATED     4   3     1
  LCE2B WILD-TYPE 303  86    71
D223V5, multiclass
       clus
vv      LCE2B MUTATED LCE2B WILD-TYPE
  N0                4             303
  N1                3              86
  N2+N3             1              71
[1] 3 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
  LCE2B MUTATED     8   0
  LCE2B WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2B MUTATED      8    0
  LCE2B WILD-TYPE  319   23
   clus
vv  LCE2B MUTATED LCE2B WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D223V7, binary
                 cls
clus                0   1
  LCE2B MUTATED     2   6
  LCE2B WILD-TYPE 257 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2B MUTATED      2    6
  LCE2B WILD-TYPE  257  215
        clus
vv       LCE2B MUTATED LCE2B WILD-TYPE
  FEMALE             2             257
  MALE               6             215
[1] 2 2
[1] FALSE
D223V8, continuous
[1] "Remove cluster labels:" "LCE2B MUTATED"         
clus
  LCE2B MUTATED LCE2B WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8281      TCGA-86-8358 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N5 
"LCE2B WILD-TYPE" "LCE2B WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LCE2B MUTATED                            0                                 3
  LCE2B WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LCE2B MUTATED                                                    5
  LCE2B WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LCE2B MUTATED                                            0
  LCE2B WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LCE2B MUTATED                                               0
  LCE2B WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  LCE2B MUTATED                                0
  LCE2B WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  LCE2B MUTATED                                    0
  LCE2B WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LCE2B MUTATED                              0                             0
  LCE2B WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LCE2B MUTATED                                               0
  LCE2B WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  LCE2B MUTATED                              0
  LCE2B WILD-TYPE                            9
D223V9, multiclass
                                                    clus
vv                                                   LCE2B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   LCE2B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V10, binary
                 cls
clus                0   1
  LCE2B MUTATED     1   7
  LCE2B WILD-TYPE  19 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2B MUTATED      1    7
  LCE2B WILD-TYPE   19  453
     clus
vv    LCE2B MUTATED LCE2B WILD-TYPE
  NO              1              19
  YES             7             453
[1] 2 2
[1] FALSE
D223V11, continuous
D223V12, continuous
                 vv
clus               R0  R1  R2  RX
  LCE2B MUTATED     6   0   0   0
  LCE2B WILD-TYPE 304  11   4  25
D223V13, multiclass
    clus
vv   LCE2B MUTATED LCE2B WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCE2B MUTATED                                  0     0
  LCE2B WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LCE2B MUTATED                           0     5
  LCE2B WILD-TYPE                        29   372
D223V14, multiclass
                                  clus
vv                                 LCE2B MUTATED LCE2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V15, binary
                 cls
clus                0   1
  LCE2B MUTATED     0   4
  LCE2B WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2B MUTATED      0    4
  LCE2B WILD-TYPE    6  345
                        clus
vv                       LCE2B MUTATED LCE2B WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(224) Variable = NTHL1 MUTATION ANALYSIS
D224V1, survival
                 sevent
clus2               0   1
  NTHL1 MUTATED     4   2
  NTHL1 WILD-TYPE 311 139
  NTHL1 MUTATED NTHL1 WILD-TYPE 
              6             450 
  NTHL1 MUTATED NTHL1 WILD-TYPE 
              2             139 
$`NTHL1 MUTATED`
TCGA-55-6971 TCGA-55-8092 TCGA-55-A48Y TCGA-55-A490 TCGA-91-8499 TCGA-93-A4JO 
        0.82         5.06        20.71         1.58         1.18         1.08 

$`NTHL1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
        3.29        19.66        19.73         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       14.27         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
       23.61        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  NTHL1 MUTATED NTHL1 WILD-TYPE 
           0.82            0.00 
  NTHL1 MUTATED NTHL1 WILD-TYPE 
          20.71          223.96 
  NTHL1 MUTATED NTHL1 WILD-TYPE 
           1.38           18.15 
[1] "0.8 - 20.7 (1.4)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "6"  
D224V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NTHL1 MUTATED         0        2        1         2         1          0
  NTHL1 WILD-TYPE       4      121      132        44        66         70
                 vv
clus              STAGE IIIB STAGE IV
  NTHL1 MUTATED            0        0
  NTHL1 WILD-TYPE         11       25
D224V3, multiclass
            clus
vv           NTHL1 MUTATED NTHL1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               1             132
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTHL1 MUTATED     2   3   1   0
  NTHL1 WILD-TYPE 153 258  42  18
D224V4, multiclass
    clus
vv   NTHL1 MUTATED NTHL1 WILD-TYPE
  T1             2             153
  T2             3             258
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  NTHL1 MUTATED     6   0     0
  NTHL1 WILD-TYPE 301  89    72
D224V5, multiclass
       clus
vv      NTHL1 MUTATED NTHL1 WILD-TYPE
  N0                6             301
  N1                0              89
  N2+N3             0              72
[1] 3 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
  NTHL1 MUTATED     1   0
  NTHL1 WILD-TYPE 326  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTHL1 MUTATED      1    0
  NTHL1 WILD-TYPE  326   23
   clus
vv  NTHL1 MUTATED NTHL1 WILD-TYPE
  0             1             326
  1             0              23
[1] 2 2
[1] FALSE
D224V7, binary
                 cls
clus                0   1
  NTHL1 MUTATED     2   4
  NTHL1 WILD-TYPE 257 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTHL1 MUTATED      2    4
  NTHL1 WILD-TYPE  257  217
        clus
vv       NTHL1 MUTATED NTHL1 WILD-TYPE
  FEMALE             2             257
  MALE               4             217
[1] 2 2
[1] FALSE
D224V8, continuous
[1] "Remove cluster labels:" "NTHL1 MUTATED"         
clus
  NTHL1 MUTATED NTHL1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-99-7458      TCGA-MN-A4N1 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"NTHL1 WILD-TYPE" "NTHL1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NTHL1 MUTATED                            0                                 1
  NTHL1 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NTHL1 MUTATED                                                    5
  NTHL1 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NTHL1 MUTATED                                            0
  NTHL1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NTHL1 MUTATED                                               0
  NTHL1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NTHL1 MUTATED                                0
  NTHL1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NTHL1 MUTATED                                    0
  NTHL1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NTHL1 MUTATED                              0                             0
  NTHL1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NTHL1 MUTATED                                               0
  NTHL1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NTHL1 MUTATED                              0
  NTHL1 WILD-TYPE                            9
D224V9, multiclass
                                                    clus
vv                                                   NTHL1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NTHL1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V10, binary
                 cls
clus                0   1
  NTHL1 MUTATED     0   6
  NTHL1 WILD-TYPE  20 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTHL1 MUTATED      0    6
  NTHL1 WILD-TYPE   20  454
     clus
vv    NTHL1 MUTATED NTHL1 WILD-TYPE
  NO              0              20
  YES             6             454
[1] 2 2
[1] FALSE
D224V11, continuous
D224V12, continuous
                 vv
clus               R0  R1  R2  RX
  NTHL1 MUTATED     4   0   0   1
  NTHL1 WILD-TYPE 306  11   4  24
D224V13, multiclass
    clus
vv   NTHL1 MUTATED NTHL1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTHL1 MUTATED                                  0     0
  NTHL1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTHL1 MUTATED                           0     6
  NTHL1 WILD-TYPE                        29   371
D224V14, multiclass
                                  clus
vv                                 NTHL1 MUTATED NTHL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V15, binary
                 cls
clus                0   1
  NTHL1 MUTATED     0   5
  NTHL1 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTHL1 MUTATED      0    5
  NTHL1 WILD-TYPE    6  344
                        clus
vv                       NTHL1 MUTATED NTHL1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(225) Variable = UBAP2 MUTATION ANALYSIS
D225V1, survival
                 sevent
clus2               0   1
  UBAP2 MUTATED     7   2
  UBAP2 WILD-TYPE 308 139
  UBAP2 MUTATED UBAP2 WILD-TYPE 
              9             447 
  UBAP2 MUTATED UBAP2 WILD-TYPE 
              2             139 
$`UBAP2 MUTATED`
TCGA-05-4398 TCGA-44-3398 TCGA-73-7499 TCGA-78-7156 TCGA-86-7701 TCGA-86-8073 
       47.05        38.24        23.51        32.09        31.13        24.33 
TCGA-93-8067 TCGA-MP-A4T4 TCGA-NJ-A4YG 
        6.12        86.04        62.60 

$`UBAP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       39.09       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  UBAP2 MUTATED UBAP2 WILD-TYPE 
           6.12            0.00 
  UBAP2 MUTATED UBAP2 WILD-TYPE 
          86.04          223.96 
  UBAP2 MUTATED UBAP2 WILD-TYPE 
          32.09           17.72 
[1] "6.1 - 86.0 (32.1)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "2.6"
D225V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  UBAP2 MUTATED         0        1        4         0         1          2
  UBAP2 WILD-TYPE       4      122      129        46        66         68
                 vv
clus              STAGE IIIB STAGE IV
  UBAP2 MUTATED            1        2
  UBAP2 WILD-TYPE         10       23
D225V3, multiclass
            clus
vv           UBAP2 MUTATED UBAP2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             2              68
  STAGE IIIB             1              10
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UBAP2 MUTATED     1   8   0   2
  UBAP2 WILD-TYPE 154 253  43  16
D225V4, multiclass
    clus
vv   UBAP2 MUTATED UBAP2 WILD-TYPE
  T1             1             154
  T2             8             253
  T3             0              43
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  UBAP2 MUTATED     6   2     3
  UBAP2 WILD-TYPE 301  87    69
D225V5, multiclass
       clus
vv      UBAP2 MUTATED UBAP2 WILD-TYPE
  N0                6             301
  N1                2              87
  N2+N3             3              69
[1] 3 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
  UBAP2 MUTATED     8   2
  UBAP2 WILD-TYPE 319  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAP2 MUTATED      8    2
  UBAP2 WILD-TYPE  319   21
   clus
vv  UBAP2 MUTATED UBAP2 WILD-TYPE
  0             8             319
  1             2              21
[1] 2 2
[1] FALSE
D225V7, binary
                 cls
clus                0   1
  UBAP2 MUTATED     5   6
  UBAP2 WILD-TYPE 254 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAP2 MUTATED      5    6
  UBAP2 WILD-TYPE  254  215
        clus
vv       UBAP2 MUTATED UBAP2 WILD-TYPE
  FEMALE             5             254
  MALE               6             215
[1] 2 2
[1] FALSE
D225V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  UBAP2 MUTATED                            0                                 3
  UBAP2 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  UBAP2 MUTATED                                                    7
  UBAP2 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  UBAP2 MUTATED                                            0
  UBAP2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  UBAP2 MUTATED                                               1
  UBAP2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  UBAP2 MUTATED                                0
  UBAP2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  UBAP2 MUTATED                                    0
  UBAP2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  UBAP2 MUTATED                              0                             0
  UBAP2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  UBAP2 MUTATED                                               0
  UBAP2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  UBAP2 MUTATED                              0
  UBAP2 WILD-TYPE                            9
D225V9, multiclass
                                                    clus
vv                                                   UBAP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   UBAP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V10, binary
                 cls
clus                0   1
  UBAP2 MUTATED     0  11
  UBAP2 WILD-TYPE  20 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAP2 MUTATED      0   11
  UBAP2 WILD-TYPE   20  449
     clus
vv    UBAP2 MUTATED UBAP2 WILD-TYPE
  NO              0              20
  YES            11             449
[1] 2 2
[1] FALSE
D225V11, continuous
D225V12, continuous
                 vv
clus               R0  R1  R2  RX
  UBAP2 MUTATED     9   0   0   1
  UBAP2 WILD-TYPE 301  11   4  24
D225V13, multiclass
    clus
vv   UBAP2 MUTATED UBAP2 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBAP2 MUTATED                                  0     1
  UBAP2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UBAP2 MUTATED                           0     7
  UBAP2 WILD-TYPE                        29   370
D225V14, multiclass
                                  clus
vv                                 UBAP2 MUTATED UBAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V15, binary
                 cls
clus                0   1
  UBAP2 MUTATED     0   5
  UBAP2 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAP2 MUTATED      0    5
  UBAP2 WILD-TYPE    6  344
                        clus
vv                       UBAP2 MUTATED UBAP2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(226) Variable = MATR3 MUTATION ANALYSIS
D226V1, survival
                 sevent
clus2               0   1
  MATR3 MUTATED     5   2
  MATR3 WILD-TYPE 310 139
  MATR3 MUTATED MATR3 WILD-TYPE 
              7             449 
  MATR3 MUTATED MATR3 WILD-TYPE 
              2             139 
$`MATR3 MUTATED`
TCGA-49-4486 TCGA-55-6712 TCGA-55-8506 TCGA-55-A4DF TCGA-62-8399 TCGA-78-8640 
       76.21         0.79         0.36        20.19        88.64       214.62 
TCGA-78-8655 
       77.59 

$`MATR3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 
       11.08        11.54        13.64        13.45        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       19.99         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
       39.35        10.55        32.68        39.75        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  MATR3 MUTATED MATR3 WILD-TYPE 
           0.36            0.00 
  MATR3 MUTATED MATR3 WILD-TYPE 
         214.62          223.96 
  MATR3 MUTATED MATR3 WILD-TYPE 
          76.21           17.92 
[1] "0.4 - 214.6 (76.2)" "0.0 - 224.0 (17.9)"
[1] "hr=" "3.4"
D226V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MATR3 MUTATED         0        3        0         2         1          1
  MATR3 WILD-TYPE       4      120      133        44        66         69
                 vv
clus              STAGE IIIB STAGE IV
  MATR3 MUTATED            0        0
  MATR3 WILD-TYPE         11       25
D226V3, multiclass
            clus
vv           MATR3 MUTATED MATR3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               0             133
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MATR3 MUTATED     4   2   1   0
  MATR3 WILD-TYPE 151 259  42  18
D226V4, multiclass
    clus
vv   MATR3 MUTATED MATR3 WILD-TYPE
  T1             4             151
  T2             2             259
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  MATR3 MUTATED     4   2     1
  MATR3 WILD-TYPE 303  87    71
D226V5, multiclass
       clus
vv      MATR3 MUTATED MATR3 WILD-TYPE
  N0                4             303
  N1                2              87
  N2+N3             1              71
[1] 3 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
  MATR3 MUTATED     4   0
  MATR3 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATR3 MUTATED      4    0
  MATR3 WILD-TYPE  323   23
   clus
vv  MATR3 MUTATED MATR3 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D226V7, binary
                 cls
clus                0   1
  MATR3 MUTATED     2   5
  MATR3 WILD-TYPE 257 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATR3 MUTATED      2    5
  MATR3 WILD-TYPE  257  216
        clus
vv       MATR3 MUTATED MATR3 WILD-TYPE
  FEMALE             2             257
  MALE               5             216
[1] 2 2
[1] FALSE
D226V8, continuous
[1] "Remove cluster labels:" "MATR3 MUTATED"         
clus
  MATR3 MUTATED MATR3 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8402      TCGA-62-A46O 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"MATR3 WILD-TYPE" "MATR3 WILD-TYPE" "MATR3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MATR3 MUTATED                            0                                 1
  MATR3 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MATR3 MUTATED                                                    5
  MATR3 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MATR3 MUTATED                                            0
  MATR3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MATR3 MUTATED                                               0
  MATR3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MATR3 MUTATED                                0
  MATR3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MATR3 MUTATED                                    0
  MATR3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MATR3 MUTATED                              0                             1
  MATR3 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MATR3 MUTATED                                               0
  MATR3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MATR3 MUTATED                              0
  MATR3 WILD-TYPE                            9
D226V9, multiclass
                                                    clus
vv                                                   MATR3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MATR3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V10, binary
                 cls
clus                0   1
  MATR3 MUTATED     0   7
  MATR3 WILD-TYPE  20 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATR3 MUTATED      0    7
  MATR3 WILD-TYPE   20  453
     clus
vv    MATR3 MUTATED MATR3 WILD-TYPE
  NO              0              20
  YES             7             453
[1] 2 2
[1] FALSE
D226V11, continuous
D226V12, continuous
                 vv
clus               R0  R1  R2  RX
  MATR3 MUTATED     6   0   0   0
  MATR3 WILD-TYPE 304  11   4  25
D226V13, multiclass
    clus
vv   MATR3 MUTATED MATR3 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MATR3 MUTATED                                  0     0
  MATR3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MATR3 MUTATED                           0     5
  MATR3 WILD-TYPE                        29   372
D226V14, multiclass
                                  clus
vv                                 MATR3 MUTATED MATR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V15, binary
                 cls
clus                0   1
  MATR3 MUTATED     0   4
  MATR3 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATR3 MUTATED      0    4
  MATR3 WILD-TYPE    6  345
                        clus
vv                       MATR3 MUTATED MATR3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(227) Variable = CD34 MUTATION ANALYSIS
D227V1, survival
                sevent
clus2              0   1
  CD34 MUTATED     7   3
  CD34 WILD-TYPE 308 138
  CD34 MUTATED CD34 WILD-TYPE 
            10            446 
  CD34 MUTATED CD34 WILD-TYPE 
             3            138 
$`CD34 MUTATED`
TCGA-38-4627 TCGA-44-8117 TCGA-44-8120 TCGA-50-5946 TCGA-53-7624 TCGA-55-7907 
       37.71        12.66         8.55        22.55        34.29         0.53 
TCGA-55-8089 TCGA-69-7973 TCGA-69-8253 TCGA-86-8672 
        3.29         7.56        14.01         0.62 

$`CD34 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
      120.79        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
       36.07        18.87        29.00        17.59        23.64         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
        6.64         6.12        22.68        13.61         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30         2.93        12.56        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  CD34 MUTATED CD34 WILD-TYPE 
          0.53           0.00 
  CD34 MUTATED CD34 WILD-TYPE 
         37.71         223.96 
  CD34 MUTATED CD34 WILD-TYPE 
        10.605         18.150 
[1] "0.5 - 37.7 (10.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.8"
D227V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CD34 MUTATED         0        2        3         3         1          0
  CD34 WILD-TYPE       4      121      130        43        66         70
                vv
clus             STAGE IIIB STAGE IV
  CD34 MUTATED            0        1
  CD34 WILD-TYPE         11       24
D227V3, multiclass
            clus
vv           CD34 MUTATED CD34 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              3            130
  STAGE IIA             3             43
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD34 MUTATED     4   5   1   0
  CD34 WILD-TYPE 151 256  42  18
D227V4, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  T1            4            151
  T2            5            256
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  CD34 MUTATED     7   3     0
  CD34 WILD-TYPE 300  86    72
D227V5, multiclass
       clus
vv      CD34 MUTATED CD34 WILD-TYPE
  N0               7            300
  N1               3             86
  N2+N3            0             72
[1] 3 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
  CD34 MUTATED     6   1
  CD34 WILD-TYPE 321  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      6    1
  CD34 WILD-TYPE  321   22
   clus
vv  CD34 MUTATED CD34 WILD-TYPE
  0            6            321
  1            1             22
[1] 2 2
[1] FALSE
D227V7, binary
                cls
clus               0   1
  CD34 MUTATED     5   5
  CD34 WILD-TYPE 254 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      5    5
  CD34 WILD-TYPE  254  216
        clus
vv       CD34 MUTATED CD34 WILD-TYPE
  FEMALE            5            254
  MALE              5            216
[1] 2 2
[1] FALSE
D227V8, continuous
[1] "Remove cluster labels:" "CD34 MUTATED"          
clus
  CD34 MUTATED CD34 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"CD34 WILD-TYPE" "CD34 WILD-TYPE" "CD34 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CD34 MUTATED                            0                                 3
  CD34 WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CD34 MUTATED                                                    7
  CD34 WILD-TYPE                                                287
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CD34 MUTATED                                            0
  CD34 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CD34 MUTATED                                               0
  CD34 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  CD34 MUTATED                                0
  CD34 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  CD34 MUTATED                                    0
  CD34 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CD34 MUTATED                              0                             0
  CD34 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CD34 MUTATED                                               0
  CD34 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  CD34 MUTATED                              0
  CD34 WILD-TYPE                            9
D227V9, multiclass
                                                    clus
vv                                                   CD34 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   CD34 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V10, binary
                cls
clus               0   1
  CD34 MUTATED     0  10
  CD34 WILD-TYPE  20 450
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      0   10
  CD34 WILD-TYPE   20  450
     clus
vv    CD34 MUTATED CD34 WILD-TYPE
  NO             0             20
  YES           10            450
[1] 2 2
[1] FALSE
D227V11, continuous
D227V12, continuous
                vv
clus              R0  R1  R2  RX
  CD34 MUTATED     5   0   0   0
  CD34 WILD-TYPE 305  11   4  25
D227V13, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD34 MUTATED                                  0     0
  CD34 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD34 MUTATED                           2     8
  CD34 WILD-TYPE                        27   369
D227V14, multiclass
                                  clus
vv                                 CD34 MUTATED CD34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V15, binary
                cls
clus               0   1
  CD34 MUTATED     1   8
  CD34 WILD-TYPE   5 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      1    8
  CD34 WILD-TYPE    5  341
                        clus
vv                       CD34 MUTATED CD34 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(228) Variable = BRD9 MUTATION ANALYSIS
D228V1, survival
                sevent
clus2              0   1
  BRD9 MUTATED     4   1
  BRD9 WILD-TYPE 311 140
  BRD9 MUTATED BRD9 WILD-TYPE 
             5            451 
  BRD9 MUTATED BRD9 WILD-TYPE 
             1            140 
$`BRD9 MUTATED`
TCGA-05-4384 TCGA-50-5930 TCGA-55-7994 TCGA-55-8089 TCGA-62-8399 
       14.01         9.27        19.82         3.29        88.64 

$`BRD9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        6.15         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       19.99         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  BRD9 MUTATED BRD9 WILD-TYPE 
          3.29           0.00 
  BRD9 MUTATED BRD9 WILD-TYPE 
         88.64         223.96 
  BRD9 MUTATED BRD9 WILD-TYPE 
         14.01          18.08 
[1] "3.3 - 88.6 (14.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2"  
D228V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BRD9 MUTATED         0        1        0         0         1          3
  BRD9 WILD-TYPE       4      122      133        46        66         67
                vv
clus             STAGE IIIB STAGE IV
  BRD9 MUTATED            0        0
  BRD9 WILD-TYPE         11       25
D228V3, multiclass
            clus
vv           BRD9 MUTATED BRD9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              0            133
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            3             67
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD9 MUTATED     1   3   1   0
  BRD9 WILD-TYPE 154 258  42  18
D228V4, multiclass
    clus
vv   BRD9 MUTATED BRD9 WILD-TYPE
  T1            1            154
  T2            3            258
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  BRD9 MUTATED     2   0     3
  BRD9 WILD-TYPE 305  89    69
D228V5, multiclass
       clus
vv      BRD9 MUTATED BRD9 WILD-TYPE
  N0               2            305
  N1               0             89
  N2+N3            3             69
[1] 3 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
  BRD9 MUTATED     4   0
  BRD9 WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD9 MUTATED      4    0
  BRD9 WILD-TYPE  323   23
   clus
vv  BRD9 MUTATED BRD9 WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D228V7, binary
                cls
clus               0   1
  BRD9 MUTATED     0   5
  BRD9 WILD-TYPE 259 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD9 MUTATED      0    5
  BRD9 WILD-TYPE  259  216
        clus
vv       BRD9 MUTATED BRD9 WILD-TYPE
  FEMALE            0            259
  MALE              5            216
[1] 2 2
[1] FALSE
D228V8, continuous
[1] "Remove cluster labels:" "BRD9 MUTATED"          
clus
  BRD9 MUTATED BRD9 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5778     TCGA-69-7974 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-69-8254     TCGA-71-6725     TCGA-71-8520     TCGA-73-4659 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4676 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8055     TCGA-86-8056 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BRD9 MUTATED                            0                                 2
  BRD9 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BRD9 MUTATED                                                    2
  BRD9 WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BRD9 MUTATED                                            0
  BRD9 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BRD9 MUTATED                                               0
  BRD9 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  BRD9 MUTATED                                0
  BRD9 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  BRD9 MUTATED                                    0
  BRD9 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BRD9 MUTATED                              0                             1
  BRD9 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BRD9 MUTATED                                               0
  BRD9 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  BRD9 MUTATED                              0
  BRD9 WILD-TYPE                            9
D228V9, multiclass
                                                    clus
vv                                                   BRD9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   BRD9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V10, binary
                cls
clus               0   1
  BRD9 MUTATED     1   4
  BRD9 WILD-TYPE  19 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD9 MUTATED      1    4
  BRD9 WILD-TYPE   19  456
     clus
vv    BRD9 MUTATED BRD9 WILD-TYPE
  NO             1             19
  YES            4            456
[1] 2 2
[1] FALSE
D228V11, continuous
D228V12, continuous
[1] "Remove cluster labels:" "BRD9 MUTATED"          
clus
  BRD9 MUTATED BRD9 WILD-TYPE 
             2            255 
    TCGA-05-4390     TCGA-05-4396     TCGA-05-4405     TCGA-05-4410 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-05-4415     TCGA-05-4417     TCGA-05-4424     TCGA-05-4427 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-05-4433     TCGA-05-5420     TCGA-05-5423     TCGA-05-5425 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-05-5428     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-7271     TCGA-38-A44F 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-3396     TCGA-44-3398 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-5644     TCGA-44-5645 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6147     TCGA-44-6148 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4494     TCGA-49-4505     TCGA-53-7624 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-1592 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-1595     TCGA-55-5899     TCGA-55-6642     TCGA-55-6712 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-6971     TCGA-55-7227     TCGA-55-7283     TCGA-55-7570 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7728     TCGA-55-7907     TCGA-55-7910 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7914     TCGA-55-8092     TCGA-55-8094 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-8096     TCGA-55-8097     TCGA-55-8205     TCGA-55-8299 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-8301     TCGA-55-8302     TCGA-55-8506     TCGA-55-8507 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8514     TCGA-55-8615 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-62-8398     TCGA-64-1677 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5774     TCGA-64-5775     TCGA-64-5778 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-64-5779     TCGA-64-5781     TCGA-69-7761     TCGA-69-7763 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-69-7764     TCGA-69-7765     TCGA-69-7974     TCGA-69-7979 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K     TCGA-73-4659 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-7498     TCGA-75-6214 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-75-7025     TCGA-75-7027     TCGA-75-7031     TCGA-78-7145 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7542 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6851     TCGA-86-7711     TCGA-86-7714 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6836 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"BRD9 WILD-TYPE" "BRD9 WILD-TYPE" "BRD9 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  BRD9 MUTATED     3   0   0   1
  BRD9 WILD-TYPE 307  11   4  24
D228V13, multiclass
    clus
vv   BRD9 MUTATED BRD9 WILD-TYPE
  R0            3            307
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD9 MUTATED                                  0     0
  BRD9 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD9 MUTATED                           0     4
  BRD9 WILD-TYPE                        29   373
D228V14, multiclass
                                  clus
vv                                 BRD9 MUTATED BRD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       4            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V15, binary
                cls
clus               0   1
  BRD9 MUTATED     0   4
  BRD9 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD9 MUTATED      0    4
  BRD9 WILD-TYPE    6  345
                        clus
vv                       BRD9 MUTATED BRD9 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(229) Variable = BTAF1 MUTATION ANALYSIS
D229V1, survival
                 sevent
clus2               0   1
  BTAF1 MUTATED    14   7
  BTAF1 WILD-TYPE 301 134
  BTAF1 MUTATED BTAF1 WILD-TYPE 
             21             435 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
              7             134 
$`BTAF1 MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4417 TCGA-05-4418 TCGA-05-4430 TCGA-44-5644 
       19.96        37.02        14.96         9.01        25.02        28.37 
TCGA-44-8120 TCGA-55-1595 TCGA-55-8302 TCGA-62-A46O TCGA-69-7765 TCGA-73-4668 
        8.55        48.62         0.76        47.80         5.42        15.35 
TCGA-78-7537 TCGA-78-8662 TCGA-86-7954 TCGA-91-6829 TCGA-91-7771 TCGA-99-8032 
       53.33       110.50        19.89        41.36        16.18         1.45 
TCGA-MN-A4N4 TCGA-MP-A4T8 TCGA-MP-A4TA 
       38.63         5.29        31.23 

$`BTAF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       29.98        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       22.03         9.04         2.04         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        6.25        26.56        33.30        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94         9.21        23.05         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        26.30         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20         8.02        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       32.68       214.62        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.43        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85        36.76         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
       86.04        58.85         5.49        41.59         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  BTAF1 MUTATED BTAF1 WILD-TYPE 
           0.76            0.00 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
         110.50          223.96 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
          19.96           17.92 
[1] "0.8 - 110.5 (20.0)" "0.0 - 224.0 (17.9)"
[1] "hr=" "1.2"
D229V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BTAF1 MUTATED         0        4       14         0         2          2
  BTAF1 WILD-TYPE       4      119      119        46        65         68
                 vv
clus              STAGE IIIB STAGE IV
  BTAF1 MUTATED            0        1
  BTAF1 WILD-TYPE         11       24
D229V3, multiclass
            clus
vv           BTAF1 MUTATED BTAF1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB              14             119
  STAGE IIA              0              46
  STAGE IIB              2              65
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTAF1 MUTATED     4  16   2   1
  BTAF1 WILD-TYPE 151 245  41  17
D229V4, multiclass
    clus
vv   BTAF1 MUTATED BTAF1 WILD-TYPE
  T1             4             151
  T2            16             245
  T3             2              41
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  BTAF1 MUTATED    20   1     2
  BTAF1 WILD-TYPE 287  88    70
D229V5, multiclass
       clus
vv      BTAF1 MUTATED BTAF1 WILD-TYPE
  N0               20             287
  N1                1              88
  N2+N3             2              70
[1] 3 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
  BTAF1 MUTATED    18   0
  BTAF1 WILD-TYPE 309  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED     18    0
  BTAF1 WILD-TYPE  309   23
   clus
vv  BTAF1 MUTATED BTAF1 WILD-TYPE
  0            18             309
  1             0              23
[1] 2 2
[1] FALSE
D229V7, binary
                 cls
clus                0   1
  BTAF1 MUTATED    11  12
  BTAF1 WILD-TYPE 248 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED     11   12
  BTAF1 WILD-TYPE  248  209
        clus
vv       BTAF1 MUTATED BTAF1 WILD-TYPE
  FEMALE            11             248
  MALE              12             209
[1] 2 2
[1] FALSE
D229V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BTAF1 MUTATED                            0                                 7
  BTAF1 WILD-TYPE                         18                                95
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BTAF1 MUTATED                                                   12
  BTAF1 WILD-TYPE                                                282
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BTAF1 MUTATED                                            0
  BTAF1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BTAF1 MUTATED                                               2
  BTAF1 WILD-TYPE                                            17
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  BTAF1 MUTATED                                1
  BTAF1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  BTAF1 MUTATED                                    1
  BTAF1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BTAF1 MUTATED                              0                             0
  BTAF1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BTAF1 MUTATED                                               0
  BTAF1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  BTAF1 MUTATED                              0
  BTAF1 WILD-TYPE                            9
D229V9, multiclass
                                                    clus
vv                                                   BTAF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  2
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   BTAF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   17
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V10, binary
                 cls
clus                0   1
  BTAF1 MUTATED     0  23
  BTAF1 WILD-TYPE  20 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED      0   23
  BTAF1 WILD-TYPE   20  437
     clus
vv    BTAF1 MUTATED BTAF1 WILD-TYPE
  NO              0              20
  YES            23             437
[1] 2 2
[1] FALSE
D229V11, continuous
D229V12, continuous
                 vv
clus               R0  R1  R2  RX
  BTAF1 MUTATED    18   0   0   0
  BTAF1 WILD-TYPE 292  11   4  25
D229V13, multiclass
    clus
vv   BTAF1 MUTATED BTAF1 WILD-TYPE
  R0            18             292
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTAF1 MUTATED                                  1     1
  BTAF1 WILD-TYPE                                0     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BTAF1 MUTATED                           2     9
  BTAF1 WILD-TYPE                        27   368
D229V14, multiclass
                                  clus
vv                                 BTAF1 MUTATED BTAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V15, binary
                 cls
clus                0   1
  BTAF1 MUTATED     0  12
  BTAF1 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED      0   12
  BTAF1 WILD-TYPE    6  337
                        clus
vv                       BTAF1 MUTATED BTAF1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(230) Variable = RGS20 MUTATION ANALYSIS
D230V1, survival
                 sevent
clus2               0   1
  RGS20 MUTATED     7   0
  RGS20 WILD-TYPE 308 141
  RGS20 MUTATED RGS20 WILD-TYPE 
              7             449 
  RGS20 MUTATED RGS20 WILD-TYPE 
              0             141 
$`RGS20 MUTATED`
TCGA-05-4424 TCGA-05-5428 TCGA-38-4625 TCGA-64-5779 TCGA-78-7539 TCGA-86-6851 
       30.02        22.03        97.74        28.41        10.75         5.88 
TCGA-86-A4JF 
       17.62 

$`RGS20 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  RGS20 MUTATED RGS20 WILD-TYPE 
           5.88            0.00 
  RGS20 MUTATED RGS20 WILD-TYPE 
          97.74          223.96 
  RGS20 MUTATED RGS20 WILD-TYPE 
          22.03           17.98 
[1] "5.9 - 97.7 (22.0)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "9300000"
D230V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RGS20 MUTATED         0        0        1         3         2          1
  RGS20 WILD-TYPE       4      123      132        43        65         69
                 vv
clus              STAGE IIIB STAGE IV
  RGS20 MUTATED            0        0
  RGS20 WILD-TYPE         11       25
D230V3, multiclass
            clus
vv           RGS20 MUTATED RGS20 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               1             132
  STAGE IIA              3              43
  STAGE IIB              2              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RGS20 MUTATED     2   3   2   0
  RGS20 WILD-TYPE 153 258  41  18
D230V4, multiclass
    clus
vv   RGS20 MUTATED RGS20 WILD-TYPE
  T1             2             153
  T2             3             258
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  RGS20 MUTATED     4   2     1
  RGS20 WILD-TYPE 303  87    71
D230V5, multiclass
       clus
vv      RGS20 MUTATED RGS20 WILD-TYPE
  N0                4             303
  N1                2              87
  N2+N3             1              71
[1] 3 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
  RGS20 MUTATED     7   0
  RGS20 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS20 MUTATED      7    0
  RGS20 WILD-TYPE  320   23
   clus
vv  RGS20 MUTATED RGS20 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D230V7, binary
                 cls
clus                0   1
  RGS20 MUTATED     3   4
  RGS20 WILD-TYPE 256 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS20 MUTATED      3    4
  RGS20 WILD-TYPE  256  217
        clus
vv       RGS20 MUTATED RGS20 WILD-TYPE
  FEMALE             3             256
  MALE               4             217
[1] 2 2
[1] FALSE
D230V8, continuous
[1] "Remove cluster labels:" "RGS20 MUTATED"         
clus
  RGS20 MUTATED RGS20 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"RGS20 WILD-TYPE" "RGS20 WILD-TYPE" "RGS20 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RGS20 MUTATED                            1                                 4
  RGS20 WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RGS20 MUTATED                                                    2
  RGS20 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RGS20 MUTATED                                            0
  RGS20 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RGS20 MUTATED                                               0
  RGS20 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RGS20 MUTATED                                0
  RGS20 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RGS20 MUTATED                                    0
  RGS20 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RGS20 MUTATED                              0                             0
  RGS20 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RGS20 MUTATED                                               0
  RGS20 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RGS20 MUTATED                              0
  RGS20 WILD-TYPE                            9
D230V9, multiclass
                                                    clus
vv                                                   RGS20 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   RGS20 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V10, binary
                 cls
clus                0   1
  RGS20 MUTATED     1   6
  RGS20 WILD-TYPE  19 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS20 MUTATED      1    6
  RGS20 WILD-TYPE   19  454
     clus
vv    RGS20 MUTATED RGS20 WILD-TYPE
  NO              1              19
  YES             6             454
[1] 2 2
[1] FALSE
D230V11, continuous
D230V12, continuous
                 vv
clus               R0  R1  R2  RX
  RGS20 MUTATED     5   1   0   0
  RGS20 WILD-TYPE 305  10   4  25
D230V13, multiclass
    clus
vv   RGS20 MUTATED RGS20 WILD-TYPE
  R0             5             305
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGS20 MUTATED                                  0     0
  RGS20 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RGS20 MUTATED                           0     5
  RGS20 WILD-TYPE                        29   372
D230V14, multiclass
                                  clus
vv                                 RGS20 MUTATED RGS20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V15, binary
                 cls
clus                0   1
  RGS20 MUTATED     0   4
  RGS20 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS20 MUTATED      0    4
  RGS20 WILD-TYPE    6  345
                        clus
vv                       RGS20 MUTATED RGS20 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(231) Variable = ITLN1 MUTATION ANALYSIS
D231V1, survival
                 sevent
clus2               0   1
  ITLN1 MUTATED     6   3
  ITLN1 WILD-TYPE 309 138
  ITLN1 MUTATED ITLN1 WILD-TYPE 
              9             447 
  ITLN1 MUTATED ITLN1 WILD-TYPE 
              3             138 
$`ITLN1 MUTATED`
TCGA-05-4382 TCGA-44-7660 TCGA-55-6642 TCGA-55-8208 TCGA-73-4659 TCGA-78-7156 
       19.96        19.46        32.65        22.16        23.38        32.09 
TCGA-78-7220 TCGA-86-8674 TCGA-97-8172 
       26.53        13.32        17.92 

$`ITLN1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        14.60        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
        9.21        23.05        48.62         2.86         0.07         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        38.50         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF 
       30.84        27.58         0.62        14.96        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
        5.95         0.59         0.72        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ITLN1 MUTATED ITLN1 WILD-TYPE 
          13.32            0.00 
  ITLN1 MUTATED ITLN1 WILD-TYPE 
          32.65          223.96 
  ITLN1 MUTATED ITLN1 WILD-TYPE 
          22.16           17.72 
[1] "13.3 - 32.6 (22.2)" "0.0 - 224.0 (17.7)"
[1] "hr=" "1.2"
D231V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ITLN1 MUTATED         0        1        4         1         0          2
  ITLN1 WILD-TYPE       4      122      129        45        67         68
                 vv
clus              STAGE IIIB STAGE IV
  ITLN1 MUTATED            0        1
  ITLN1 WILD-TYPE         11       24
D231V3, multiclass
            clus
vv           ITLN1 MUTATED ITLN1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              0              67
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITLN1 MUTATED     1   7   0   1
  ITLN1 WILD-TYPE 154 254  43  17
D231V4, multiclass
    clus
vv   ITLN1 MUTATED ITLN1 WILD-TYPE
  T1             1             154
  T2             7             254
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  ITLN1 MUTATED     5   2     2
  ITLN1 WILD-TYPE 302  87    70
D231V5, multiclass
       clus
vv      ITLN1 MUTATED ITLN1 WILD-TYPE
  N0                5             302
  N1                2              87
  N2+N3             2              70
[1] 3 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
  ITLN1 MUTATED     6   1
  ITLN1 WILD-TYPE 321  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITLN1 MUTATED      6    1
  ITLN1 WILD-TYPE  321   22
   clus
vv  ITLN1 MUTATED ITLN1 WILD-TYPE
  0             6             321
  1             1              22
[1] 2 2
[1] FALSE
D231V7, binary
                 cls
clus                0   1
  ITLN1 MUTATED     3   6
  ITLN1 WILD-TYPE 256 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITLN1 MUTATED      3    6
  ITLN1 WILD-TYPE  256  215
        clus
vv       ITLN1 MUTATED ITLN1 WILD-TYPE
  FEMALE             3             256
  MALE               6             215
[1] 2 2
[1] FALSE
D231V8, continuous
[1] "Remove cluster labels:" "ITLN1 MUTATED"         
clus
  ITLN1 MUTATED ITLN1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"ITLN1 WILD-TYPE" "ITLN1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ITLN1 MUTATED                            1                                 3
  ITLN1 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ITLN1 MUTATED                                                    4
  ITLN1 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ITLN1 MUTATED                                            0
  ITLN1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ITLN1 MUTATED                                               0
  ITLN1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ITLN1 MUTATED                                0
  ITLN1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ITLN1 MUTATED                                    0
  ITLN1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ITLN1 MUTATED                              0                             1
  ITLN1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ITLN1 MUTATED                                               0
  ITLN1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ITLN1 MUTATED                              0
  ITLN1 WILD-TYPE                            9
D231V9, multiclass
                                                    clus
vv                                                   ITLN1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ITLN1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V10, binary
                 cls
clus                0   1
  ITLN1 MUTATED     1   8
  ITLN1 WILD-TYPE  19 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITLN1 MUTATED      1    8
  ITLN1 WILD-TYPE   19  452
     clus
vv    ITLN1 MUTATED ITLN1 WILD-TYPE
  NO              1              19
  YES             8             452
[1] 2 2
[1] FALSE
D231V11, continuous
D231V12, continuous
                 vv
clus               R0  R1  R2  RX
  ITLN1 MUTATED     7   0   0   0
  ITLN1 WILD-TYPE 303  11   4  25
D231V13, multiclass
    clus
vv   ITLN1 MUTATED ITLN1 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITLN1 MUTATED                                  0     0
  ITLN1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITLN1 MUTATED                           0     8
  ITLN1 WILD-TYPE                        29   369
D231V14, multiclass
                                  clus
vv                                 ITLN1 MUTATED ITLN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V15, binary
                 cls
clus                0   1
  ITLN1 MUTATED     0   5
  ITLN1 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITLN1 MUTATED      0    5
  ITLN1 WILD-TYPE    6  344
                        clus
vv                       ITLN1 MUTATED ITLN1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(232) Variable = FIGNL1 MUTATION ANALYSIS
D232V1, survival
                  sevent
clus2                0   1
  FIGNL1 MUTATED     5   5
  FIGNL1 WILD-TYPE 310 136
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              10              446 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               5              136 
$`FIGNL1 MUTATED`
TCGA-05-4396 TCGA-05-4424 TCGA-05-4427 TCGA-50-5072 TCGA-55-7227 TCGA-55-7994 
        9.96        30.02        26.01         8.22         1.74        19.82 
TCGA-55-8090 TCGA-55-A4DF TCGA-64-5781 TCGA-MP-A4TK 
       19.66        20.19        51.25        19.13 

$`FIGNL1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        14.66        14.10        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            1.74             0.00 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
           51.25           223.96 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
          19.740           17.835 
[1] "1.7 - 51.2 (19.7)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "2"  
D232V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FIGNL1 MUTATED         0        2        2         0         4          2
  FIGNL1 WILD-TYPE       4      121      131        46        63         68
                  vv
clus               STAGE IIIB STAGE IV
  FIGNL1 MUTATED            1        0
  FIGNL1 WILD-TYPE         10       25
D232V3, multiclass
            clus
vv           FIGNL1 MUTATED FIGNL1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                2              131
  STAGE IIA               0               46
  STAGE IIB               4               63
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   5   3   1
  FIGNL1 WILD-TYPE 153 256  40  17
D232V4, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  T1              2              153
  T2              5              256
  T3              3               40
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  FIGNL1 MUTATED     6   4     1
  FIGNL1 WILD-TYPE 301  85    71
D232V5, multiclass
       clus
vv      FIGNL1 MUTATED FIGNL1 WILD-TYPE
  N0                 6              301
  N1                 4               85
  N2+N3              1               71
[1] 3 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
  FIGNL1 MUTATED     7   0
  FIGNL1 WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      7    0
  FIGNL1 WILD-TYPE  320   23
   clus
vv  FIGNL1 MUTATED FIGNL1 WILD-TYPE
  0              7              320
  1              0               23
[1] 2 2
[1] FALSE
D232V7, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     3   8
  FIGNL1 WILD-TYPE 256 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      3    8
  FIGNL1 WILD-TYPE  256  213
        clus
vv       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  FEMALE              3              256
  MALE                8              213
[1] 2 2
[1] FALSE
D232V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FIGNL1 MUTATED                            0                                 5
  FIGNL1 WILD-TYPE                         18                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FIGNL1 MUTATED                                                    6
  FIGNL1 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FIGNL1 MUTATED                                            0
  FIGNL1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FIGNL1 MUTATED                                               0
  FIGNL1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  FIGNL1 MUTATED                                0
  FIGNL1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  FIGNL1 MUTATED                                    0
  FIGNL1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FIGNL1 MUTATED                              0                             0
  FIGNL1 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FIGNL1 MUTATED                                               0
  FIGNL1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  FIGNL1 MUTATED                              0
  FIGNL1 WILD-TYPE                            9
D232V9, multiclass
                                                    clus
vv                                                   FIGNL1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   FIGNL1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V10, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     1  10
  FIGNL1 WILD-TYPE  19 450
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      1   10
  FIGNL1 WILD-TYPE   19  450
     clus
vv    FIGNL1 MUTATED FIGNL1 WILD-TYPE
  NO               1               19
  YES             10              450
[1] 2 2
[1] FALSE
D232V11, continuous
D232V12, continuous
                  vv
clus                R0  R1  R2  RX
  FIGNL1 MUTATED     7   1   0   1
  FIGNL1 WILD-TYPE 303  10   4  24
D232V13, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  R0              7              303
  R1              1               10
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FIGNL1 MUTATED                                  0     0
  FIGNL1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FIGNL1 MUTATED                           0     6
  FIGNL1 WILD-TYPE                        29   371
D232V14, multiclass
                                  clus
vv                                 FIGNL1 MUTATED FIGNL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         6              371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V15, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     0   6
  FIGNL1 WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      0    6
  FIGNL1 WILD-TYPE    6  343
                        clus
vv                       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              343
[1] 2 2
[1] FALSE

Clustering(233) Variable = ABCF3 MUTATION ANALYSIS
D233V1, survival
                 sevent
clus2               0   1
  ABCF3 MUTATED     5   2
  ABCF3 WILD-TYPE 310 139
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              7             449 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              2             139 
$`ABCF3 MUTATED`
TCGA-55-7815 TCGA-55-7994 TCGA-55-A4DF TCGA-62-A46V TCGA-78-8648 TCGA-91-6830 
        1.78        19.82        20.19        72.30        39.75         1.97 
TCGA-95-8494 
        2.76 

$`ABCF3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        1.12         0.79         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       67.96        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 
       10.75        39.35        10.55        32.68       214.62        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
       18.67        12.39        15.68        15.65        27.29        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ABCF3 MUTATED ABCF3 WILD-TYPE 
           1.78            0.00 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
          72.30          223.96 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
          19.82           17.98 
[1] "1.8 - 72.3 (19.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D233V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ABCF3 MUTATED         0        1        3         2         2          0
  ABCF3 WILD-TYPE       4      122      130        44        65         70
                 vv
clus              STAGE IIIB STAGE IV
  ABCF3 MUTATED            0        0
  ABCF3 WILD-TYPE         11       25
D233V3, multiclass
            clus
vv           ABCF3 MUTATED ABCF3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              2              44
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCF3 MUTATED     2   4   2   0
  ABCF3 WILD-TYPE 153 257  41  18
D233V4, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  T1             2             153
  T2             4             257
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ABCF3 MUTATED     6   2     0
  ABCF3 WILD-TYPE 301  87    72
D233V5, multiclass
       clus
vv      ABCF3 MUTATED ABCF3 WILD-TYPE
  N0                6             301
  N1                2              87
  N2+N3             0              72
[1] 3 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
  ABCF3 MUTATED     4   0
  ABCF3 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      4    0
  ABCF3 WILD-TYPE  323   23
   clus
vv  ABCF3 MUTATED ABCF3 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D233V7, binary
                 cls
clus                0   1
  ABCF3 MUTATED     3   5
  ABCF3 WILD-TYPE 256 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      3    5
  ABCF3 WILD-TYPE  256  216
        clus
vv       ABCF3 MUTATED ABCF3 WILD-TYPE
  FEMALE             3             256
  MALE               5             216
[1] 2 2
[1] FALSE
D233V8, continuous
[1] "Remove cluster labels:" "ABCF3 MUTATED"         
clus
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ABCF3 MUTATED                            0                                 2
  ABCF3 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ABCF3 MUTATED                                                    6
  ABCF3 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ABCF3 MUTATED                                            0
  ABCF3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ABCF3 MUTATED                                               0
  ABCF3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ABCF3 MUTATED                                0
  ABCF3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ABCF3 MUTATED                                    0
  ABCF3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ABCF3 MUTATED                              0                             0
  ABCF3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ABCF3 MUTATED                                               0
  ABCF3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ABCF3 MUTATED                              0
  ABCF3 WILD-TYPE                            9
D233V9, multiclass
                                                    clus
vv                                                   ABCF3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ABCF3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V10, binary
                 cls
clus                0   1
  ABCF3 MUTATED     0   8
  ABCF3 WILD-TYPE  20 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      0    8
  ABCF3 WILD-TYPE   20  452
     clus
vv    ABCF3 MUTATED ABCF3 WILD-TYPE
  NO              0              20
  YES             8             452
[1] 2 2
[1] FALSE
D233V11, continuous
D233V12, continuous
                 vv
clus               R0  R1  R2  RX
  ABCF3 MUTATED     5   0   0   1
  ABCF3 WILD-TYPE 305  11   4  24
D233V13, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCF3 MUTATED                                  0     0
  ABCF3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCF3 MUTATED                           0     5
  ABCF3 WILD-TYPE                        29   372
D233V14, multiclass
                                  clus
vv                                 ABCF3 MUTATED ABCF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V15, binary
                 cls
clus                0   1
  ABCF3 MUTATED     0   5
  ABCF3 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      0    5
  ABCF3 WILD-TYPE    6  344
                        clus
vv                       ABCF3 MUTATED ABCF3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(234) Variable = KSR1 MUTATION ANALYSIS
D234V1, survival
                sevent
clus2              0   1
  KSR1 MUTATED    10   2
  KSR1 WILD-TYPE 305 139
  KSR1 MUTATED KSR1 WILD-TYPE 
            12            444 
  KSR1 MUTATED KSR1 WILD-TYPE 
             2            139 
$`KSR1 MUTATED`
TCGA-05-4389 TCGA-05-5428 TCGA-44-7670 TCGA-44-8117 TCGA-44-A4SU TCGA-49-4487 
       45.01        22.03        29.00        12.66        13.45        28.11 
TCGA-69-7765 TCGA-69-7979 TCGA-78-8640 TCGA-86-8674 TCGA-91-8496 TCGA-MN-A4N5 
        5.42         2.93       214.62        13.32        16.60         2.76 

$`KSR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       18.87        17.59        23.64         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.64        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       13.87         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        14.96        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.18        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19        38.63        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  KSR1 MUTATED KSR1 WILD-TYPE 
          2.76           0.00 
  KSR1 MUTATED KSR1 WILD-TYPE 
        214.62         223.96 
  KSR1 MUTATED KSR1 WILD-TYPE 
        15.025         18.100 
[1] "2.8 - 214.6 (15.0)" "0.0 - 224.0 (18.1)"
[1] "hr=" "2.4"
D234V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KSR1 MUTATED         0        4        3         4         0          0
  KSR1 WILD-TYPE       4      119      130        42        67         70
                vv
clus             STAGE IIIB STAGE IV
  KSR1 MUTATED            0        1
  KSR1 WILD-TYPE         11       24
D234V3, multiclass
            clus
vv           KSR1 MUTATED KSR1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              3            130
  STAGE IIA             4             42
  STAGE IIB             0             67
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KSR1 MUTATED     7   4   0   1
  KSR1 WILD-TYPE 148 257  43  17
D234V4, multiclass
    clus
vv   KSR1 MUTATED KSR1 WILD-TYPE
  T1            7            148
  T2            4            257
  T3            0             43
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  KSR1 MUTATED     7   4     0
  KSR1 WILD-TYPE 300  85    72
D234V5, multiclass
       clus
vv      KSR1 MUTATED KSR1 WILD-TYPE
  N0               7            300
  N1               4             85
  N2+N3            0             72
[1] 3 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
  KSR1 MUTATED     8   0
  KSR1 WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR1 MUTATED      8    0
  KSR1 WILD-TYPE  319   23
   clus
vv  KSR1 MUTATED KSR1 WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D234V7, binary
                cls
clus               0   1
  KSR1 MUTATED     6   6
  KSR1 WILD-TYPE 253 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR1 MUTATED      6    6
  KSR1 WILD-TYPE  253  215
        clus
vv       KSR1 MUTATED KSR1 WILD-TYPE
  FEMALE            6            253
  MALE              6            215
[1] 2 2
[1] FALSE
D234V8, continuous
[1] "Remove cluster labels:" "KSR1 MUTATED"          
clus
  KSR1 MUTATED KSR1 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7711 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7954     TCGA-86-7955 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8074     TCGA-86-8075 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8281 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
    TCGA-99-7458     TCGA-MN-A4N1     TCGA-MN-A4N4 
"KSR1 WILD-TYPE" "KSR1 WILD-TYPE" "KSR1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KSR1 MUTATED                            1                                 3
  KSR1 WILD-TYPE                         17                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KSR1 MUTATED                                                    6
  KSR1 WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KSR1 MUTATED                                            0
  KSR1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KSR1 MUTATED                                               1
  KSR1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  KSR1 MUTATED                                0
  KSR1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  KSR1 MUTATED                                    0
  KSR1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KSR1 MUTATED                              0                             1
  KSR1 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KSR1 MUTATED                                               0
  KSR1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  KSR1 MUTATED                              0
  KSR1 WILD-TYPE                            9
D234V9, multiclass
                                                    clus
vv                                                   KSR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   KSR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V10, binary
                cls
clus               0   1
  KSR1 MUTATED     0  12
  KSR1 WILD-TYPE  20 448
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR1 MUTATED      0   12
  KSR1 WILD-TYPE   20  448
     clus
vv    KSR1 MUTATED KSR1 WILD-TYPE
  NO             0             20
  YES           12            448
[1] 2 2
[1] FALSE
D234V11, continuous
D234V12, continuous
                vv
clus              R0  R1  R2  RX
  KSR1 MUTATED     7   0   0   0
  KSR1 WILD-TYPE 303  11   4  25
D234V13, multiclass
    clus
vv   KSR1 MUTATED KSR1 WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KSR1 MUTATED                                  0     0
  KSR1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KSR1 MUTATED                           1     8
  KSR1 WILD-TYPE                        28   369
D234V14, multiclass
                                  clus
vv                                 KSR1 MUTATED KSR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V15, binary
                cls
clus               0   1
  KSR1 MUTATED     1   8
  KSR1 WILD-TYPE   5 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR1 MUTATED      1    8
  KSR1 WILD-TYPE    5  341
                        clus
vv                       KSR1 MUTATED KSR1 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(235) Variable = ARAP3 MUTATION ANALYSIS
D235V1, survival
                 sevent
clus2               0   1
  ARAP3 MUTATED     9   8
  ARAP3 WILD-TYPE 306 133
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             17             439 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              8             133 
$`ARAP3 MUTATED`
TCGA-05-4382 TCGA-38-4625 TCGA-44-7669 TCGA-44-A47F TCGA-50-6590 TCGA-55-A494 
       19.96        97.74        18.87        11.08        42.35        15.81 
TCGA-62-A46O TCGA-64-5779 TCGA-69-7979 TCGA-73-4658 TCGA-73-4668 TCGA-78-7167 
       47.80        28.41         2.93        52.60        15.35        88.14 
TCGA-78-7537 TCGA-91-6830 TCGA-91-8497 TCGA-97-A4M0 TCGA-O1-A52J 
       53.33         1.97        14.27        21.44        59.11 

$`ARAP3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58        19.59         0.92        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        42.90        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        2.01         0.10        23.38        29.98        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20         8.02        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
       17.62        13.64        26.47        10.62        41.36        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R 
       19.82 

  ARAP3 MUTATED ARAP3 WILD-TYPE 
           1.97            0.00 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          97.74          223.96 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          21.44           17.75 
[1] "2.0 - 97.7 (21.4)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D235V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARAP3 MUTATED         0        2        9         2         2          1
  ARAP3 WILD-TYPE       4      121      124        44        65         69
                 vv
clus              STAGE IIIB STAGE IV
  ARAP3 MUTATED            0        1
  ARAP3 WILD-TYPE         11       24
D235V3, multiclass
            clus
vv           ARAP3 MUTATED ARAP3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               9             124
  STAGE IIA              2              44
  STAGE IIB              2              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARAP3 MUTATED     4  13   0   0
  ARAP3 WILD-TYPE 151 248  43  18
D235V4, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  T1             4             151
  T2            13             248
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ARAP3 MUTATED    12   4     1
  ARAP3 WILD-TYPE 295  85    71
D235V5, multiclass
       clus
vv      ARAP3 MUTATED ARAP3 WILD-TYPE
  N0               12             295
  N1                4              85
  N2+N3             1              71
[1] 3 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
  ARAP3 MUTATED    10   1
  ARAP3 WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     10    1
  ARAP3 WILD-TYPE  317   22
   clus
vv  ARAP3 MUTATED ARAP3 WILD-TYPE
  0            10             317
  1             1              22
[1] 2 2
[1] FALSE
D235V7, binary
                 cls
clus                0   1
  ARAP3 MUTATED    11   6
  ARAP3 WILD-TYPE 248 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     11    6
  ARAP3 WILD-TYPE  248  215
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  FEMALE            11             248
  MALE               6             215
[1] 2 2
[1] FALSE
D235V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARAP3 MUTATED                            2                                 3
  ARAP3 WILD-TYPE                         16                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARAP3 MUTATED                                                   10
  ARAP3 WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARAP3 MUTATED                                            0
  ARAP3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARAP3 MUTATED                                               0
  ARAP3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ARAP3 MUTATED                                0
  ARAP3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ARAP3 MUTATED                                    1
  ARAP3 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARAP3 MUTATED                              0                             1
  ARAP3 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARAP3 MUTATED                                               0
  ARAP3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ARAP3 MUTATED                              0
  ARAP3 WILD-TYPE                            9
D235V9, multiclass
                                                    clus
vv                                                   ARAP3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ARAP3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V10, binary
                 cls
clus                0   1
  ARAP3 MUTATED     1  16
  ARAP3 WILD-TYPE  19 444
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      1   16
  ARAP3 WILD-TYPE   19  444
     clus
vv    ARAP3 MUTATED ARAP3 WILD-TYPE
  NO              1              19
  YES            16             444
[1] 2 2
[1] FALSE
D235V11, continuous
D235V12, continuous
                 vv
clus               R0  R1  R2  RX
  ARAP3 MUTATED     9   0   0   0
  ARAP3 WILD-TYPE 301  11   4  25
D235V13, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARAP3 MUTATED                                  1     0
  ARAP3 WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARAP3 MUTATED                           1    13
  ARAP3 WILD-TYPE                        28   364
D235V14, multiclass
                                  clus
vv                                 ARAP3 MUTATED ARAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       13             364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V15, binary
                 cls
clus                0   1
  ARAP3 MUTATED     0  14
  ARAP3 WILD-TYPE   6 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      0   14
  ARAP3 WILD-TYPE    6  335
                        clus
vv                       ARAP3 MUTATED ARAP3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            14             335
[1] 2 2
[1] FALSE

Clustering(236) Variable = IPO9 MUTATION ANALYSIS
D236V1, survival
                sevent
clus2              0   1
  IPO9 MUTATED     5   4
  IPO9 WILD-TYPE 310 137
  IPO9 MUTATED IPO9 WILD-TYPE 
             9            447 
  IPO9 MUTATED IPO9 WILD-TYPE 
             4            137 
$`IPO9 MUTATED`
TCGA-05-4382 TCGA-49-6745 TCGA-55-6968 TCGA-55-8207 TCGA-69-7974 TCGA-78-7147 
       19.96        17.16        42.51         2.17         6.05        19.27 
TCGA-78-8662 TCGA-91-6829 TCGA-NJ-A4YQ 
      110.50        41.36        29.13 

$`IPO9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       17.62        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13         1.64         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  IPO9 MUTATED IPO9 WILD-TYPE 
          2.17           0.00 
  IPO9 MUTATED IPO9 WILD-TYPE 
        110.50         223.96 
  IPO9 MUTATED IPO9 WILD-TYPE 
         19.96          17.92 
[1] "2.2 - 110.5 (20.0)" "0.0 - 224.0 (17.9)"
[1] "hr=" "1.1"
D236V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IPO9 MUTATED         0        1        4         0         1          2
  IPO9 WILD-TYPE       4      122      129        46        66         68
                vv
clus             STAGE IIIB STAGE IV
  IPO9 MUTATED            0        1
  IPO9 WILD-TYPE         11       24
D236V3, multiclass
            clus
vv           IPO9 MUTATED IPO9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              4            129
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IPO9 MUTATED     2   7   0   0
  IPO9 WILD-TYPE 153 254  43  18
D236V4, multiclass
    clus
vv   IPO9 MUTATED IPO9 WILD-TYPE
  T1            2            153
  T2            7            254
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  IPO9 MUTATED     6   1     2
  IPO9 WILD-TYPE 301  88    70
D236V5, multiclass
       clus
vv      IPO9 MUTATED IPO9 WILD-TYPE
  N0               6            301
  N1               1             88
  N2+N3            2             70
[1] 3 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
  IPO9 MUTATED     5   1
  IPO9 WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO9 MUTATED      5    1
  IPO9 WILD-TYPE  322   22
   clus
vv  IPO9 MUTATED IPO9 WILD-TYPE
  0            5            322
  1            1             22
[1] 2 2
[1] FALSE
D236V7, binary
                cls
clus               0   1
  IPO9 MUTATED     4   5
  IPO9 WILD-TYPE 255 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO9 MUTATED      4    5
  IPO9 WILD-TYPE  255  216
        clus
vv       IPO9 MUTATED IPO9 WILD-TYPE
  FEMALE            4            255
  MALE              5            216
[1] 2 2
[1] FALSE
D236V8, continuous
[1] "Remove cluster labels:" "IPO9 MUTATED"          
clus
  IPO9 MUTATED IPO9 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"IPO9 WILD-TYPE" "IPO9 WILD-TYPE" "IPO9 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  IPO9 MUTATED                            1                                 2
  IPO9 WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IPO9 MUTATED                                                    5
  IPO9 WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IPO9 MUTATED                                            0
  IPO9 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IPO9 MUTATED                                               1
  IPO9 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  IPO9 MUTATED                                0
  IPO9 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  IPO9 MUTATED                                    0
  IPO9 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  IPO9 MUTATED                              0                             0
  IPO9 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IPO9 MUTATED                                               0
  IPO9 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  IPO9 MUTATED                              0
  IPO9 WILD-TYPE                            9
D236V9, multiclass
                                                    clus
vv                                                   IPO9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   IPO9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V10, binary
                cls
clus               0   1
  IPO9 MUTATED     1   8
  IPO9 WILD-TYPE  19 452
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO9 MUTATED      1    8
  IPO9 WILD-TYPE   19  452
     clus
vv    IPO9 MUTATED IPO9 WILD-TYPE
  NO             1             19
  YES            8            452
[1] 2 2
[1] FALSE
D236V11, continuous
D236V12, continuous
                vv
clus              R0  R1  R2  RX
  IPO9 MUTATED     5   0   0   1
  IPO9 WILD-TYPE 305  11   4  24
D236V13, multiclass
    clus
vv   IPO9 MUTATED IPO9 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IPO9 MUTATED                                  0     0
  IPO9 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IPO9 MUTATED                           0     7
  IPO9 WILD-TYPE                        29   370
D236V14, multiclass
                                  clus
vv                                 IPO9 MUTATED IPO9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V15, binary
                cls
clus               0   1
  IPO9 MUTATED     0   5
  IPO9 WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO9 MUTATED      0    5
  IPO9 WILD-TYPE    6  344
                        clus
vv                       IPO9 MUTATED IPO9 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(237) Variable = SLC26A4 MUTATION ANALYSIS
D237V1, survival
                   sevent
clus2                 0   1
  SLC26A4 MUTATED     8   2
  SLC26A4 WILD-TYPE 307 139
  SLC26A4 MUTATED SLC26A4 WILD-TYPE 
               10               446 
  SLC26A4 MUTATED SLC26A4 WILD-TYPE 
                2               139 
$`SLC26A4 MUTATED`
TCGA-05-4398 TCGA-44-6778 TCGA-50-6592 TCGA-55-7570 TCGA-55-8506 TCGA-69-7978 
       47.05        61.28        25.55         0.20         0.36         2.30 
TCGA-78-7152 TCGA-91-6829 TCGA-91-6847 TCGA-L9-A443 
       39.52        41.36        27.68         3.81 

$`SLC26A4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 
       29.03        25.12        22.55        42.35         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1.15         7.99         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
        5.69        19.27        20.58        35.93        21.90        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       17.62        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SLC26A4 MUTATED SLC26A4 WILD-TYPE 
              0.2               0.0 
  SLC26A4 MUTATED SLC26A4 WILD-TYPE 
            61.28            223.96 
  SLC26A4 MUTATED SLC26A4 WILD-TYPE 
           26.615            17.950 
[1] "0.2 - 61.3 (26.6)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.9"
D237V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC26A4 MUTATED         0        4        4         0         2          0
  SLC26A4 WILD-TYPE       4      119      129        46        65         70
                   vv
clus                STAGE IIIB STAGE IV
  SLC26A4 MUTATED            1        0
  SLC26A4 WILD-TYPE         10       25
D237V3, multiclass
            clus
vv           SLC26A4 MUTATED SLC26A4 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 4               119
  STAGE IB                 4               129
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               0                70
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A4 MUTATED     4   5   1   1
  SLC26A4 WILD-TYPE 151 256  42  17
D237V4, multiclass
    clus
vv   SLC26A4 MUTATED SLC26A4 WILD-TYPE
  T1               4               151
  T2               5               256
  T3               1                42
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  SLC26A4 MUTATED     9   1     1
  SLC26A4 WILD-TYPE 298  88    71
D237V5, multiclass
       clus
vv      SLC26A4 MUTATED SLC26A4 WILD-TYPE
  N0                  9               298
  N1                  1                88
  N2+N3               1                71
[1] 3 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
  SLC26A4 MUTATED     4   0
  SLC26A4 WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A4 MUTATED      4    0
  SLC26A4 WILD-TYPE  323   23
   clus
vv  SLC26A4 MUTATED SLC26A4 WILD-TYPE
  0               4               323
  1               0                23
[1] 2 2
[1] FALSE
D237V7, binary
                   cls
clus                  0   1
  SLC26A4 MUTATED     6   5
  SLC26A4 WILD-TYPE 253 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A4 MUTATED      6    5
  SLC26A4 WILD-TYPE  253  216
        clus
vv       SLC26A4 MUTATED SLC26A4 WILD-TYPE
  FEMALE               6               253
  MALE                 5               216
[1] 2 2
[1] FALSE
D237V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC26A4 MUTATED                            0
  SLC26A4 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC26A4 MUTATED                                   3
  SLC26A4 WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC26A4 MUTATED                                                    7
  SLC26A4 WILD-TYPE                                                287
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC26A4 MUTATED                                            0
  SLC26A4 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC26A4 MUTATED                                               1
  SLC26A4 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC26A4 MUTATED                                0
  SLC26A4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC26A4 MUTATED                                    0
  SLC26A4 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC26A4 MUTATED                              0                             0
  SLC26A4 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC26A4 MUTATED                                               0
  SLC26A4 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC26A4 MUTATED                              0
  SLC26A4 WILD-TYPE                            9
D237V9, multiclass
                                                    clus
vv                                                   SLC26A4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SLC26A4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V10, binary
                   cls
clus                  0   1
  SLC26A4 MUTATED     0  11
  SLC26A4 WILD-TYPE  20 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A4 MUTATED      0   11
  SLC26A4 WILD-TYPE   20  449
     clus
vv    SLC26A4 MUTATED SLC26A4 WILD-TYPE
  NO                0                20
  YES              11               449
[1] 2 2
[1] FALSE
D237V11, continuous
D237V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC26A4 MUTATED     7   0   0   0
  SLC26A4 WILD-TYPE 303  11   4  25
D237V13, multiclass
    clus
vv   SLC26A4 MUTATED SLC26A4 WILD-TYPE
  R0               7               303
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC26A4 MUTATED                                  0     0
  SLC26A4 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC26A4 MUTATED                           2     7
  SLC26A4 WILD-TYPE                        27   370
D237V14, multiclass
                                  clus
vv                                 SLC26A4 MUTATED SLC26A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                          7               370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V15, binary
                   cls
clus                  0   1
  SLC26A4 MUTATED     0   7
  SLC26A4 WILD-TYPE   6 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A4 MUTATED      0    7
  SLC26A4 WILD-TYPE    6  342
                        clus
vv                       SLC26A4 MUTATED SLC26A4 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               7               342
[1] 2 2
[1] FALSE

Clustering(238) Variable = MOCOS MUTATION ANALYSIS
D238V1, survival
                 sevent
clus2               0   1
  MOCOS MUTATED     7   2
  MOCOS WILD-TYPE 308 139
  MOCOS MUTATED MOCOS WILD-TYPE 
              9             447 
  MOCOS MUTATED MOCOS WILD-TYPE 
              2             139 
$`MOCOS MUTATED`
TCGA-05-4402 TCGA-44-6775 TCGA-44-6777 TCGA-53-A4EZ TCGA-55-A490 TCGA-86-8076 
        8.02        23.18        32.45         9.21         1.58        16.08 
TCGA-91-6835 TCGA-97-7554 TCGA-MN-A4N4 
        2.60        25.48        38.63 

$`MOCOS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
       27.78        23.15        21.63        63.72        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
        7.59        27.25        34.29        30.54        13.94        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MOCOS MUTATED MOCOS WILD-TYPE 
           1.58            0.00 
  MOCOS MUTATED MOCOS WILD-TYPE 
          38.63          223.96 
  MOCOS MUTATED MOCOS WILD-TYPE 
          16.08           18.08 
[1] "1.6 - 38.6 (16.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D238V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MOCOS MUTATED         0        3        2         2         0          1
  MOCOS WILD-TYPE       4      120      131        44        67         69
                 vv
clus              STAGE IIIB STAGE IV
  MOCOS MUTATED            0        1
  MOCOS WILD-TYPE         11       24
D238V3, multiclass
            clus
vv           MOCOS MUTATED MOCOS WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               2             131
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MOCOS MUTATED     3   6   0   0
  MOCOS WILD-TYPE 152 255  43  18
D238V4, multiclass
    clus
vv   MOCOS MUTATED MOCOS WILD-TYPE
  T1             3             152
  T2             6             255
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  MOCOS MUTATED     5   1     1
  MOCOS WILD-TYPE 302  88    71
D238V5, multiclass
       clus
vv      MOCOS MUTATED MOCOS WILD-TYPE
  N0                5             302
  N1                1              88
  N2+N3             1              71
[1] 3 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
  MOCOS MUTATED     4   1
  MOCOS WILD-TYPE 323  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCOS MUTATED      4    1
  MOCOS WILD-TYPE  323   22
   clus
vv  MOCOS MUTATED MOCOS WILD-TYPE
  0             4             323
  1             1              22
[1] 2 2
[1] FALSE
D238V7, binary
                 cls
clus                0   1
  MOCOS MUTATED     5   4
  MOCOS WILD-TYPE 254 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCOS MUTATED      5    4
  MOCOS WILD-TYPE  254  217
        clus
vv       MOCOS MUTATED MOCOS WILD-TYPE
  FEMALE             5             254
  MALE               4             217
[1] 2 2
[1] FALSE
D238V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MOCOS MUTATED                            1                                 1
  MOCOS WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MOCOS MUTATED                                                    5
  MOCOS WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MOCOS MUTATED                                            0
  MOCOS WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MOCOS MUTATED                                               0
  MOCOS WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MOCOS MUTATED                                0
  MOCOS WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MOCOS MUTATED                                    0
  MOCOS WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MOCOS MUTATED                              0                             2
  MOCOS WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MOCOS MUTATED                                               0
  MOCOS WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MOCOS MUTATED                              0
  MOCOS WILD-TYPE                            9
D238V9, multiclass
                                                    clus
vv                                                   MOCOS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MOCOS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V10, binary
                 cls
clus                0   1
  MOCOS MUTATED     1   8
  MOCOS WILD-TYPE  19 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCOS MUTATED      1    8
  MOCOS WILD-TYPE   19  452
     clus
vv    MOCOS MUTATED MOCOS WILD-TYPE
  NO              1              19
  YES             8             452
[1] 2 2
[1] FALSE
D238V11, continuous
D238V12, continuous
                 vv
clus               R0  R1  R2  RX
  MOCOS MUTATED     5   0   1   2
  MOCOS WILD-TYPE 305  11   3  23
D238V13, multiclass
    clus
vv   MOCOS MUTATED MOCOS WILD-TYPE
  R0             5             305
  R1             0              11
  R2             1               3
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOCOS MUTATED                                  0     0
  MOCOS WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MOCOS MUTATED                           0     8
  MOCOS WILD-TYPE                        29   369
D238V14, multiclass
                                  clus
vv                                 MOCOS MUTATED MOCOS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V15, binary
                 cls
clus                0   1
  MOCOS MUTATED     2   5
  MOCOS WILD-TYPE   4 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCOS MUTATED      2    5
  MOCOS WILD-TYPE    4  344
                        clus
vv                       MOCOS MUTATED MOCOS WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(239) Variable = MOGAT2 MUTATION ANALYSIS
D239V1, survival
                  sevent
clus2                0   1
  MOGAT2 MUTATED     4   1
  MOGAT2 WILD-TYPE 311 140
  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
               5              451 
  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
               1              140 
$`MOGAT2 MUTATED`
TCGA-05-4397 TCGA-44-6147 TCGA-55-8089 TCGA-95-7567 TCGA-99-8032 
       24.03        27.78         3.29        18.67         1.45 

$`MOGAT2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         1.22         2.86        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85        36.76         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
            1.45             0.00 
  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
           27.78           223.96 
  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
           18.67            17.98 
[1] "1.4 - 27.8 (18.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D239V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MOGAT2 MUTATED         0        3        2         0         2          1
  MOGAT2 WILD-TYPE       4      120      131        46        65         69
                  vv
clus               STAGE IIIB STAGE IV
  MOGAT2 MUTATED            0        0
  MOGAT2 WILD-TYPE         11       25
D239V3, multiclass
            clus
vv           MOGAT2 MUTATED MOGAT2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                2              131
  STAGE IIA               0               46
  STAGE IIB               2               65
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MOGAT2 MUTATED     3   5   0   0
  MOGAT2 WILD-TYPE 152 256  43  18
D239V4, multiclass
    clus
vv   MOGAT2 MUTATED MOGAT2 WILD-TYPE
  T1              3              152
  T2              5              256
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  MOGAT2 MUTATED     4   2     1
  MOGAT2 WILD-TYPE 303  87    71
D239V5, multiclass
       clus
vv      MOGAT2 MUTATED MOGAT2 WILD-TYPE
  N0                 4              303
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  MOGAT2 MUTATED     8   0
  MOGAT2 WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT2 MUTATED      8    0
  MOGAT2 WILD-TYPE  319   23
   clus
vv  MOGAT2 MUTATED MOGAT2 WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D239V7, binary
                  cls
clus                 0   1
  MOGAT2 MUTATED     3   5
  MOGAT2 WILD-TYPE 256 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT2 MUTATED      3    5
  MOGAT2 WILD-TYPE  256  216
        clus
vv       MOGAT2 MUTATED MOGAT2 WILD-TYPE
  FEMALE              3              256
  MALE                5              216
[1] 2 2
[1] FALSE
D239V8, continuous
[1] "Remove cluster labels:" "MOGAT2 MUTATED"        
clus
  MOGAT2 MUTATED MOGAT2 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8096       TCGA-55-8205       TCGA-55-8208 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" "MOGAT2 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MOGAT2 MUTATED                            0                                 2
  MOGAT2 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MOGAT2 MUTATED                                                    6
  MOGAT2 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MOGAT2 MUTATED                                            0
  MOGAT2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MOGAT2 MUTATED                                               0
  MOGAT2 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  MOGAT2 MUTATED                                0
  MOGAT2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  MOGAT2 MUTATED                                    0
  MOGAT2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MOGAT2 MUTATED                              0                             0
  MOGAT2 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MOGAT2 MUTATED                                               0
  MOGAT2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  MOGAT2 MUTATED                              0
  MOGAT2 WILD-TYPE                            9
D239V9, multiclass
                                                    clus
vv                                                   MOGAT2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   MOGAT2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V10, binary
                  cls
clus                 0   1
  MOGAT2 MUTATED     0   8
  MOGAT2 WILD-TYPE  20 452
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT2 MUTATED      0    8
  MOGAT2 WILD-TYPE   20  452
     clus
vv    MOGAT2 MUTATED MOGAT2 WILD-TYPE
  NO               0               20
  YES              8              452
[1] 2 2
[1] FALSE
D239V11, continuous
D239V12, continuous
                  vv
clus                R0  R1  R2  RX
  MOGAT2 MUTATED     6   0   0   0
  MOGAT2 WILD-TYPE 304  11   4  25
D239V13, multiclass
    clus
vv   MOGAT2 MUTATED MOGAT2 WILD-TYPE
  R0              6              304
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOGAT2 MUTATED                                  0     0
  MOGAT2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MOGAT2 MUTATED                           0     4
  MOGAT2 WILD-TYPE                        29   373
D239V14, multiclass
                                  clus
vv                                 MOGAT2 MUTATED MOGAT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         4              373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V15, binary
                  cls
clus                 0   1
  MOGAT2 MUTATED     0   4
  MOGAT2 WILD-TYPE   6 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT2 MUTATED      0    4
  MOGAT2 WILD-TYPE    6  345
                        clus
vv                       MOGAT2 MUTATED MOGAT2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(240) Variable = ZKSCAN5 MUTATION ANALYSIS
D240V1, survival
                   sevent
clus2                 0   1
  ZKSCAN5 MUTATED     6   1
  ZKSCAN5 WILD-TYPE 309 140
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                7               449 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                1               140 
$`ZKSCAN5 MUTATED`
TCGA-35-4123 TCGA-49-6767 TCGA-55-8302 TCGA-55-A4DF TCGA-64-5781 TCGA-69-7979 
        5.98        22.26         0.76        20.19        51.25         2.93 
TCGA-95-7039 
        1.12 

$`ZKSCAN5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.30        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
             0.76              0.00 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
            51.25            223.96 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
             5.98             18.08 
[1] "0.8 - 51.2 (6.0)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D240V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZKSCAN5 MUTATED         0        2        3         0         2          0
  ZKSCAN5 WILD-TYPE       4      121      130        46        65         70
                   vv
clus                STAGE IIIB STAGE IV
  ZKSCAN5 MUTATED            0        0
  ZKSCAN5 WILD-TYPE         11       25
D240V3, multiclass
            clus
vv           ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 3               130
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   3   2   0
  ZKSCAN5 WILD-TYPE 153 258  41  18
D240V4, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  T1               2               153
  T2               3               258
  T3               2                41
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  ZKSCAN5 MUTATED     7   0     0
  ZKSCAN5 WILD-TYPE 300  89    72
D240V5, multiclass
       clus
vv      ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  N0                  7               300
  N1                  0                89
  N2+N3               0                72
[1] 3 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
  ZKSCAN5 MUTATED     2   0
  ZKSCAN5 WILD-TYPE 325  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      2    0
  ZKSCAN5 WILD-TYPE  325   23
   clus
vv  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  0               2               325
  1               0                23
[1] 2 2
[1] FALSE
D240V7, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     4   3
  ZKSCAN5 WILD-TYPE 255 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      4    3
  ZKSCAN5 WILD-TYPE  255  218
        clus
vv       ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  FEMALE               4               255
  MALE                 3               218
[1] 2 2
[1] FALSE
D240V8, continuous
[1] "Remove cluster labels:" "ZKSCAN5 MUTATED"       
clus
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-5375        TCGA-53-A4EZ        TCGA-55-7283 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7725        TCGA-55-7910        TCGA-55-7914 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-55-8089        TCGA-55-8096        TCGA-55-8205        TCGA-55-8208 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8511        TCGA-55-8512 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" "ZKSCAN5 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ZKSCAN5 MUTATED                            1
  ZKSCAN5 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZKSCAN5 MUTATED                                   2
  ZKSCAN5 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZKSCAN5 MUTATED                                                    4
  ZKSCAN5 WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZKSCAN5 MUTATED                                            0
  ZKSCAN5 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZKSCAN5 MUTATED                                               0
  ZKSCAN5 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ZKSCAN5 MUTATED                                0
  ZKSCAN5 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ZKSCAN5 MUTATED                                    0
  ZKSCAN5 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZKSCAN5 MUTATED                              0                             0
  ZKSCAN5 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZKSCAN5 MUTATED                                               0
  ZKSCAN5 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ZKSCAN5 MUTATED                              0
  ZKSCAN5 WILD-TYPE                            9
D240V9, multiclass
                                                    clus
vv                                                   ZKSCAN5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ZKSCAN5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V10, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     0   7
  ZKSCAN5 WILD-TYPE  20 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      0    7
  ZKSCAN5 WILD-TYPE   20  453
     clus
vv    ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  NO                0                20
  YES               7               453
[1] 2 2
[1] FALSE
D240V11, continuous
D240V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN5 MUTATED     5   0   0   0
  ZKSCAN5 WILD-TYPE 305  11   4  25
D240V13, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  R0               5               305
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZKSCAN5 MUTATED                                  0     0
  ZKSCAN5 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZKSCAN5 MUTATED                           0     7
  ZKSCAN5 WILD-TYPE                        29   370
D240V14, multiclass
                                  clus
vv                                 ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          7               370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V15, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     0   5
  ZKSCAN5 WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      0    5
  ZKSCAN5 WILD-TYPE    6  344
                        clus
vv                       ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(241) Variable = GPR150 MUTATION ANALYSIS
D241V1, survival
                  sevent
clus2                0   1
  GPR150 MUTATED     1   2
  GPR150 WILD-TYPE 314 139
  GPR150 MUTATED GPR150 WILD-TYPE 
               3              453 
  GPR150 MUTATED GPR150 WILD-TYPE 
               2              139 
$`GPR150 MUTATED`
TCGA-50-6594 TCGA-95-7039 TCGA-MP-A4TC 
       12.16         1.12         2.43 

$`GPR150 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        11.05         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59        31.23        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  GPR150 MUTATED GPR150 WILD-TYPE 
            1.12             0.00 
  GPR150 MUTATED GPR150 WILD-TYPE 
           12.16           223.96 
  GPR150 MUTATED GPR150 WILD-TYPE 
            2.43            18.12 
[1] "1.1 - 12.2 (2.4)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "13" 
D241V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GPR150 MUTATED         0        0        0         0         1          2
  GPR150 WILD-TYPE       4      123      133        46        66         68
                  vv
clus               STAGE IIIB STAGE IV
  GPR150 MUTATED            0        0
  GPR150 WILD-TYPE         11       25
D241V3, multiclass
            clus
vv           GPR150 MUTATED GPR150 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0              123
  STAGE IB                0              133
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR150 MUTATED     1   0   2   0
  GPR150 WILD-TYPE 154 261  41  18
D241V4, multiclass
    clus
vv   GPR150 MUTATED GPR150 WILD-TYPE
  T1              1              154
  T2              0              261
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  GPR150 MUTATED     1   0     2
  GPR150 WILD-TYPE 306  89    70
D241V5, multiclass
       clus
vv      GPR150 MUTATED GPR150 WILD-TYPE
  N0                 1              306
  N1                 0               89
  N2+N3              2               70
[1] 3 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
  GPR150 MUTATED     2   0
  GPR150 WILD-TYPE 325  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR150 MUTATED      2    0
  GPR150 WILD-TYPE  325   23
   clus
vv  GPR150 MUTATED GPR150 WILD-TYPE
  0              2              325
  1              0               23
[1] 2 2
[1] FALSE
D241V7, binary
                  cls
clus                 0   1
  GPR150 MUTATED     2   1
  GPR150 WILD-TYPE 257 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR150 MUTATED      2    1
  GPR150 WILD-TYPE  257  220
        clus
vv       GPR150 MUTATED GPR150 WILD-TYPE
  FEMALE              2              257
  MALE                1              220
[1] 2 2
[1] FALSE
D241V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GPR150 MUTATED                            0                                 1
  GPR150 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GPR150 MUTATED                                                    2
  GPR150 WILD-TYPE                                                292
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GPR150 MUTATED                                            0
  GPR150 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GPR150 MUTATED                                               0
  GPR150 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  GPR150 MUTATED                                0
  GPR150 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  GPR150 MUTATED                                    0
  GPR150 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GPR150 MUTATED                              0                             0
  GPR150 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GPR150 MUTATED                                               0
  GPR150 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  GPR150 MUTATED                              0
  GPR150 WILD-TYPE                            9
D241V9, multiclass
                                                    clus
vv                                                   GPR150 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   GPR150 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V10, binary
                  cls
clus                 0   1
  GPR150 MUTATED     0   3
  GPR150 WILD-TYPE  20 457
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR150 MUTATED      0    3
  GPR150 WILD-TYPE   20  457
     clus
vv    GPR150 MUTATED GPR150 WILD-TYPE
  NO               0               20
  YES              3              457
[1] 2 2
[1] FALSE
D241V11, continuous
[1] "Remove cluster labels:" "GPR150 MUTATED"        
clus
  GPR150 MUTATED GPR150 WILD-TYPE 
               2              331 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-05-4382 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4384       TCGA-05-4389       TCGA-05-4390       TCGA-05-4396 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4397       TCGA-05-4398       TCGA-05-4405       TCGA-05-4410 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4415       TCGA-05-4417       TCGA-05-4418       TCGA-05-4420 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4422       TCGA-05-4424       TCGA-05-4425       TCGA-05-4426 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4427       TCGA-05-4430       TCGA-05-4432       TCGA-05-4433 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4434       TCGA-05-5420       TCGA-05-5423       TCGA-05-5425 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-5428       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-38-4625       TCGA-38-4626       TCGA-38-4629       TCGA-38-4631 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-7271       TCGA-38-A44F       TCGA-44-2656 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-3396       TCGA-44-3398       TCGA-44-3918 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-4112       TCGA-44-5643       TCGA-44-5644       TCGA-44-5645 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6145       TCGA-44-6146       TCGA-44-6148 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-6774       TCGA-44-6775       TCGA-44-6776       TCGA-44-6777 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-6778       TCGA-44-6779       TCGA-44-7659       TCGA-44-7660 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-7661       TCGA-44-7662       TCGA-44-7667       TCGA-44-7669 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-7670       TCGA-44-7672       TCGA-44-8117       TCGA-44-8119 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-A47F       TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4490       TCGA-49-4494 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-4505       TCGA-49-4506       TCGA-49-4507       TCGA-49-4510 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-4514       TCGA-49-6742       TCGA-49-6743       TCGA-49-6744 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-6745       TCGA-49-6761       TCGA-49-6767       TCGA-50-5051 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-50-5072       TCGA-50-5931       TCGA-50-5939       TCGA-50-5941 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-50-5942       TCGA-50-6590       TCGA-50-7109       TCGA-50-8457 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-50-8459       TCGA-53-7624       TCGA-53-7626       TCGA-53-7813 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-6543       TCGA-55-6971       TCGA-55-6983 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-6985       TCGA-55-7281       TCGA-55-7283       TCGA-55-7574 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7724       TCGA-55-7725       TCGA-55-7726       TCGA-55-7728 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7903       TCGA-55-7907       TCGA-55-7910       TCGA-55-7911 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-7994       TCGA-55-7995       TCGA-55-8089 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8096       TCGA-55-8097 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8205       TCGA-55-8208       TCGA-55-8299 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8301       TCGA-55-8302       TCGA-55-8507       TCGA-55-8511 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-8621       TCGA-55-A48X       TCGA-55-A48Y 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491       TCGA-55-A492 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-A493       TCGA-55-A494       TCGA-55-A4DF       TCGA-55-A4DG 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-A46O       TCGA-62-A46P 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A470       TCGA-62-A471 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1676       TCGA-64-1677       TCGA-64-1679 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-64-5774       TCGA-64-5775       TCGA-64-5778       TCGA-64-5779 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-64-5781       TCGA-64-5815       TCGA-69-7761       TCGA-69-7763 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-69-7764       TCGA-69-7973       TCGA-69-7974       TCGA-69-7978 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-69-7979       TCGA-69-7980       TCGA-69-8253       TCGA-69-8254 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-69-8255       TCGA-69-A59K       TCGA-73-4658       TCGA-73-4659 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4670 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-73-4675       TCGA-73-4676       TCGA-73-7498       TCGA-75-5122 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-5125       TCGA-75-5126       TCGA-75-6203       TCGA-75-6206 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-6207       TCGA-75-6211       TCGA-75-6214       TCGA-75-7027 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-7031       TCGA-78-7145       TCGA-78-7146       TCGA-78-7147 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7148       TCGA-78-7149       TCGA-78-7150       TCGA-78-7152 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7153       TCGA-78-7154       TCGA-78-7155       TCGA-78-7156 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7158       TCGA-78-7159       TCGA-78-7160       TCGA-78-7161 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7162       TCGA-78-7163       TCGA-78-7166       TCGA-78-7167 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7220       TCGA-78-7535       TCGA-78-7536       TCGA-78-7537 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7539       TCGA-78-7542       TCGA-78-7633       TCGA-78-8640 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-8648       TCGA-78-8655       TCGA-78-8660       TCGA-78-8662 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-80-5607       TCGA-80-5608       TCGA-80-5611       TCGA-83-5908 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-6851       TCGA-86-7701       TCGA-86-7711       TCGA-86-7714 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-8054       TCGA-86-8055       TCGA-86-8056 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8281       TCGA-86-8358 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8669       TCGA-86-8673       TCGA-86-8674 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6830       TCGA-91-6835       TCGA-91-6836 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-91-6840       TCGA-91-6849       TCGA-91-7771       TCGA-91-8499 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-91-A4BC       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7043       TCGA-95-7562 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-95-7944       TCGA-95-7947       TCGA-95-7948       TCGA-95-A4VK 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-95-A4VN       TCGA-95-A4VP       TCGA-97-7546       TCGA-97-7547 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-7552       TCGA-97-7553       TCGA-97-7554       TCGA-97-7937 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-7938       TCGA-97-7941       TCGA-97-8171       TCGA-97-8172 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-8174       TCGA-97-8176       TCGA-97-8179       TCGA-97-A4LX 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M2       TCGA-97-A4M3 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-A4M5       TCGA-97-A4M7       TCGA-99-7458       TCGA-99-8025 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-99-8028       TCGA-99-8032       TCGA-J2-8194       TCGA-J2-A4AD 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6       TCGA-L9-A443 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-L9-A444       TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T7 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4T8       TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TD 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YF       TCGA-NJ-A4YG 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-NJ-A4YI       TCGA-NJ-A4YP       TCGA-NJ-A4YQ       TCGA-NJ-A55A 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-NJ-A55O       TCGA-NJ-A55R       TCGA-O1-A52J 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
D241V12, continuous
[1] "Remove cluster labels:" "GPR150 MUTATED"        
clus
  GPR150 MUTATED GPR150 WILD-TYPE 
               1              256 
      TCGA-05-4384       TCGA-05-4390       TCGA-05-4396       TCGA-05-4405 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4410       TCGA-05-4415       TCGA-05-4417       TCGA-05-4424 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4427       TCGA-05-4433       TCGA-05-5420       TCGA-05-5423 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-5425       TCGA-05-5428       TCGA-35-4122       TCGA-35-4123 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-35-5375       TCGA-38-4625       TCGA-38-4626       TCGA-38-7271 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-38-A44F       TCGA-44-2656       TCGA-44-2657       TCGA-44-3396 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-3398       TCGA-44-3918       TCGA-44-4112       TCGA-44-5644 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-5645       TCGA-44-6144       TCGA-44-6145       TCGA-44-6147 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-6148       TCGA-44-6774       TCGA-44-6775       TCGA-44-6776 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-6777       TCGA-44-6778       TCGA-44-6779       TCGA-44-7659 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-7660       TCGA-44-7661       TCGA-44-7662       TCGA-44-7667 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-7669       TCGA-44-7670       TCGA-44-7672       TCGA-44-8117 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-8119       TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-A47B       TCGA-44-A47F       TCGA-44-A47G       TCGA-44-A4SS 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-A4SU       TCGA-49-4486       TCGA-49-4494       TCGA-49-4505 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-53-7624       TCGA-53-7626       TCGA-53-7813       TCGA-53-A4EZ 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-1592       TCGA-55-1595       TCGA-55-5899       TCGA-55-6642 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-6712       TCGA-55-6971       TCGA-55-7227       TCGA-55-7283 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7570       TCGA-55-7574       TCGA-55-7576       TCGA-55-7724 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7728       TCGA-55-7907 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7911       TCGA-55-7914       TCGA-55-8089 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8096       TCGA-55-8097 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8205       TCGA-55-8299       TCGA-55-8301       TCGA-55-8302 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8506       TCGA-55-8507       TCGA-55-8511       TCGA-55-8512 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8514       TCGA-55-8615       TCGA-55-8620       TCGA-55-8621 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A493       TCGA-55-A494 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-8398       TCGA-64-1677       TCGA-64-1681       TCGA-64-5774 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-64-5779       TCGA-64-5781 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-69-7761       TCGA-69-7763       TCGA-69-7764       TCGA-69-7765 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-7979       TCGA-69-8253       TCGA-69-8255 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-69-A59K       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4670       TCGA-73-4675       TCGA-73-4676 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-73-7498       TCGA-75-6214       TCGA-75-7025       TCGA-75-7027 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-7031       TCGA-78-7145       TCGA-78-7146       TCGA-78-7147 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7148       TCGA-78-7149       TCGA-78-7150       TCGA-78-7152 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7153       TCGA-78-7154       TCGA-78-7155       TCGA-78-7156 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7158       TCGA-78-7159       TCGA-78-7160       TCGA-78-7161 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7162       TCGA-78-7163       TCGA-78-7166       TCGA-78-7167 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7220       TCGA-78-7535       TCGA-78-7536       TCGA-78-7537 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7539       TCGA-78-7542       TCGA-78-7633       TCGA-78-8640 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-8648       TCGA-78-8655       TCGA-78-8660       TCGA-78-8662 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-80-5607       TCGA-80-5608       TCGA-83-5908       TCGA-86-6851 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-7711       TCGA-86-7714       TCGA-86-7954       TCGA-86-8054 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8073       TCGA-86-8074 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8281       TCGA-86-8358       TCGA-86-8359       TCGA-86-8669 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8673       TCGA-86-8674       TCGA-86-A456       TCGA-91-6829 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-91-6830       TCGA-91-6836       TCGA-91-6840       TCGA-91-6849 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-91-8499       TCGA-91-A4BC       TCGA-93-7347       TCGA-93-7348 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JQ 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-95-7043       TCGA-95-7562       TCGA-95-7567       TCGA-95-7944 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-95-7947       TCGA-95-7948       TCGA-95-A4VK       TCGA-95-A4VN 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-95-A4VP       TCGA-97-7546       TCGA-97-7553       TCGA-97-7554 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-7941       TCGA-97-8171       TCGA-97-8172       TCGA-97-8174 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-8176       TCGA-97-8179       TCGA-97-A4LX       TCGA-97-A4M0 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-A4M1       TCGA-97-A4M2       TCGA-97-A4M3       TCGA-97-A4M5 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-A4M7       TCGA-99-7458       TCGA-99-8025       TCGA-99-8028 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-99-8032       TCGA-J2-8194       TCGA-J2-A4AD       TCGA-J2-A4AG 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-L4-A4E5       TCGA-L4-A4E6       TCGA-L9-A443       TCGA-L9-A444 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5       TCGA-MP-A4SV 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4SW       TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T7 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4T8       TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TE 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A4TK 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A5C7       TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-O1-A52J 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  GPR150 MUTATED     1   0   0   0
  GPR150 WILD-TYPE 309  11   4  25
D241V13, multiclass
[1] "Remove cluster labels:" "GPR150 MUTATED"        
clus
  GPR150 MUTATED GPR150 WILD-TYPE 
               1              349 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-05-4382 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4384       TCGA-05-4389       TCGA-05-4390       TCGA-05-4395 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4396       TCGA-05-4397       TCGA-05-4398       TCGA-05-4402 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4403       TCGA-05-4405       TCGA-05-4410       TCGA-05-4415 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4417       TCGA-05-4418       TCGA-05-4420       TCGA-05-4422 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4424       TCGA-05-4425       TCGA-05-4426       TCGA-05-4427 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-4430       TCGA-05-4432       TCGA-05-4433       TCGA-05-4434 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-5420       TCGA-05-5423       TCGA-05-5425       TCGA-05-5428 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-05-5429       TCGA-05-5715       TCGA-35-4122       TCGA-35-4123 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-35-5375       TCGA-38-4625       TCGA-38-4626       TCGA-38-4627 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-38-4628       TCGA-38-4629       TCGA-38-4630       TCGA-38-4631 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-6178       TCGA-38-7271       TCGA-38-A44F 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2661       TCGA-44-2665       TCGA-44-3396 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-3398       TCGA-44-3918       TCGA-44-3919       TCGA-44-4112 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6148       TCGA-44-6775       TCGA-44-A479 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SU 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4488       TCGA-49-4494 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-4501       TCGA-49-4505       TCGA-49-4506       TCGA-49-4507 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-4510       TCGA-49-4512       TCGA-49-4514       TCGA-49-6742 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-49-6744       TCGA-49-6761       TCGA-49-6767       TCGA-50-5051 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-50-5055       TCGA-50-5066       TCGA-50-5931       TCGA-50-5942 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-50-5944       TCGA-50-6593       TCGA-50-6597       TCGA-50-6673 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-50-8460       TCGA-53-7624       TCGA-53-7626       TCGA-53-A4EZ 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-1592       TCGA-55-5899       TCGA-55-6642       TCGA-55-6970 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-6971       TCGA-55-6972       TCGA-55-6980       TCGA-55-6981 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-6983       TCGA-55-6985       TCGA-55-7281       TCGA-55-7284 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7570       TCGA-55-7574       TCGA-55-7576       TCGA-55-7724 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7727       TCGA-55-7728 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7815       TCGA-55-7903       TCGA-55-7907       TCGA-55-7910 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-7911       TCGA-55-7914       TCGA-55-7994       TCGA-55-7995 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8085       TCGA-55-8087       TCGA-55-8089       TCGA-55-8090 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8091       TCGA-55-8092       TCGA-55-8094       TCGA-55-8097 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8206 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8207       TCGA-55-8208       TCGA-55-8299       TCGA-55-8301 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8302       TCGA-55-8505       TCGA-55-8506       TCGA-55-8507 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8510       TCGA-55-8511       TCGA-55-8512 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8513       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-8616       TCGA-55-8619       TCGA-55-8620       TCGA-55-8621 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A493       TCGA-55-A494 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-55-A4DF       TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1676       TCGA-64-1677 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-64-1679       TCGA-64-1681       TCGA-64-5774       TCGA-64-5775 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-64-5778       TCGA-64-5779       TCGA-64-5781       TCGA-64-5815 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-67-3771       TCGA-67-3773       TCGA-67-4679       TCGA-67-6215 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-67-6216       TCGA-67-6217       TCGA-71-6725       TCGA-71-8520 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-73-4658       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4670       TCGA-73-4675       TCGA-73-4676 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-73-4677       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-5125       TCGA-75-5126       TCGA-75-5146       TCGA-75-5147 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-6203       TCGA-75-6205       TCGA-75-6206       TCGA-75-6207 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-6211       TCGA-75-6212       TCGA-75-6214       TCGA-75-7025 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-75-7027       TCGA-75-7030       TCGA-75-7031       TCGA-78-7143 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7145       TCGA-78-7146       TCGA-78-7147       TCGA-78-7148 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7149       TCGA-78-7150       TCGA-78-7152       TCGA-78-7153 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7154       TCGA-78-7155       TCGA-78-7156       TCGA-78-7158 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7159       TCGA-78-7160       TCGA-78-7161       TCGA-78-7162 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7163       TCGA-78-7166       TCGA-78-7167       TCGA-78-7220 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7535       TCGA-78-7536       TCGA-78-7537       TCGA-78-7539 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-7540       TCGA-78-7542       TCGA-78-7633       TCGA-78-8640 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-78-8648       TCGA-78-8655       TCGA-78-8660       TCGA-78-8662 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-80-5607       TCGA-80-5608       TCGA-80-5611       TCGA-83-5908 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-6562       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7953       TCGA-86-7954       TCGA-86-7955 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8054       TCGA-86-8055       TCGA-86-8056       TCGA-86-8073 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8280       TCGA-86-8358       TCGA-86-8359 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8585       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-8672       TCGA-86-8673       TCGA-86-8674       TCGA-86-A456 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6828       TCGA-91-6829 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-91-6835       TCGA-91-6840       TCGA-91-A4BD       TCGA-93-7347 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-93-7348       TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-93-A4JP       TCGA-93-A4JQ       TCGA-95-7562       TCGA-95-7944 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-95-7947       TCGA-95-7948       TCGA-95-8039       TCGA-95-A4VK 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-95-A4VN       TCGA-97-7546       TCGA-97-7554       TCGA-97-7938 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-97-7941       TCGA-97-8176       TCGA-97-A4M2       TCGA-97-A4M7 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-99-8033       TCGA-J2-A4AD       TCGA-J2-A4AE       TCGA-J2-A4AG 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-L4-A4E5       TCGA-L4-A4E6       TCGA-L9-A443       TCGA-L9-A444 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5       TCGA-MP-A4SV 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4SW       TCGA-MP-A4SY       TCGA-MP-A4T2       TCGA-MP-A4T4 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4T6       TCGA-MP-A4T7       TCGA-MP-A4T8       TCGA-MP-A4T9 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4TA       TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A4TK       TCGA-MP-A5C7 
"GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" "GPR150 WILD-TYPE" 
      TCGA-NJ-A4YQ 
"GPR150 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR150 MUTATED                                  0     0
  GPR150 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR150 MUTATED                           1     2
  GPR150 WILD-TYPE                        28   375
D241V14, multiclass
                                  clus
vv                                 GPR150 MUTATED GPR150 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         2              375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V15, binary
                  cls
clus                 0   1
  GPR150 MUTATED     0   3
  GPR150 WILD-TYPE   6 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR150 MUTATED      0    3
  GPR150 WILD-TYPE    6  346
                        clus
vv                       GPR150 MUTATED GPR150 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              3              346
[1] 2 2
[1] FALSE

Clustering(242) Variable = MGAT5B MUTATION ANALYSIS
D242V1, survival
                  sevent
clus2                0   1
  MGAT5B MUTATED    15   3
  MGAT5B WILD-TYPE 300 138
  MGAT5B MUTATED MGAT5B WILD-TYPE 
              18              438 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
               3              138 
$`MGAT5B MUTATED`
TCGA-05-4427 TCGA-05-5429 TCGA-44-3918 TCGA-44-6778 TCGA-44-7660 TCGA-44-8117 
       26.01         9.04        34.06        61.28        19.46        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-55-1595 TCGA-55-7907 TCGA-55-8089 TCGA-55-A492 
        8.55        15.98        48.62         0.53         3.29        19.59 
TCGA-62-8399 TCGA-78-7149 TCGA-78-7155 TCGA-86-8585 TCGA-86-8673 TCGA-95-7562 
       88.64        35.93        38.50         1.15        14.96         2.86 

$`MGAT5B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 
       15.02        15.02         4.96        29.00        22.03         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        32.45        16.44        14.60 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
       23.64         3.25        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       21.47        14.60        13.91        30.84        27.58         0.62 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MGAT5B MUTATED MGAT5B WILD-TYPE 
            0.53             0.00 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
           88.64           223.96 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
           17.72            18.03 
[1] "0.5 - 88.6 (17.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.1"
D242V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MGAT5B MUTATED         0        5        8         2         1          2
  MGAT5B WILD-TYPE       4      118      125        44        66         68
                  vv
clus               STAGE IIIB STAGE IV
  MGAT5B MUTATED            1        0
  MGAT5B WILD-TYPE         10       25
D242V3, multiclass
            clus
vv           MGAT5B MUTATED MGAT5B WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              118
  STAGE IB                8              125
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MGAT5B MUTATED     5  12   1   1
  MGAT5B WILD-TYPE 150 249  42  17
D242V4, multiclass
    clus
vv   MGAT5B MUTATED MGAT5B WILD-TYPE
  T1              5              150
  T2             12              249
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  MGAT5B MUTATED    14   3     2
  MGAT5B WILD-TYPE 293  86    70
D242V5, multiclass
       clus
vv      MGAT5B MUTATED MGAT5B WILD-TYPE
  N0                14              293
  N1                 3               86
  N2+N3              2               70
[1] 3 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
  MGAT5B MUTATED    14   0
  MGAT5B WILD-TYPE 313  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED     14    0
  MGAT5B WILD-TYPE  313   23
   clus
vv  MGAT5B MUTATED MGAT5B WILD-TYPE
  0             14              313
  1              0               23
[1] 2 2
[1] FALSE
D242V7, binary
                  cls
clus                 0   1
  MGAT5B MUTATED     6  13
  MGAT5B WILD-TYPE 253 208
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      6   13
  MGAT5B WILD-TYPE  253  208
        clus
vv       MGAT5B MUTATED MGAT5B WILD-TYPE
  FEMALE              6              253
  MALE               13              208
[1] 2 2
[1] FALSE
D242V8, continuous
[1] "Remove cluster labels:" "MGAT5B MUTATED"        
clus
  MGAT5B MUTATED MGAT5B WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8096       TCGA-55-8205       TCGA-55-8208 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5778       TCGA-69-7974 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4676 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"MGAT5B WILD-TYPE" "MGAT5B WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MGAT5B MUTATED                            0                                 2
  MGAT5B WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MGAT5B MUTATED                                                   13
  MGAT5B WILD-TYPE                                                281
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MGAT5B MUTATED                                            0
  MGAT5B WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MGAT5B MUTATED                                               1
  MGAT5B WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  MGAT5B MUTATED                                1
  MGAT5B WILD-TYPE                              1
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  MGAT5B MUTATED                                    0
  MGAT5B WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MGAT5B MUTATED                              0                             1
  MGAT5B WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MGAT5B MUTATED                                               1
  MGAT5B WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  MGAT5B MUTATED                              0
  MGAT5B WILD-TYPE                            9
D242V9, multiclass
                                                    clus
vv                                                   MGAT5B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   MGAT5B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V10, binary
                  cls
clus                 0   1
  MGAT5B MUTATED     0  19
  MGAT5B WILD-TYPE  20 441
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      0   19
  MGAT5B WILD-TYPE   20  441
     clus
vv    MGAT5B MUTATED MGAT5B WILD-TYPE
  NO               0               20
  YES             19              441
[1] 2 2
[1] FALSE
D242V11, continuous
D242V12, continuous
                  vv
clus                R0  R1  R2  RX
  MGAT5B MUTATED    13   0   0   1
  MGAT5B WILD-TYPE 297  11   4  24
D242V13, multiclass
    clus
vv   MGAT5B MUTATED MGAT5B WILD-TYPE
  R0             13              297
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGAT5B MUTATED                                  0     1
  MGAT5B WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MGAT5B MUTATED                           4    11
  MGAT5B WILD-TYPE                        25   366
D242V14, multiclass
                                  clus
vv                                 MGAT5B MUTATED MGAT5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     4               25
  WHITE                                        11              366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V15, binary
                  cls
clus                 0   1
  MGAT5B MUTATED     0  13
  MGAT5B WILD-TYPE   6 336
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      0   13
  MGAT5B WILD-TYPE    6  336
                        clus
vv                       MGAT5B MUTATED MGAT5B WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             13              336
[1] 2 2
[1] FALSE

Clustering(243) Variable = AGXT MUTATION ANALYSIS
D243V1, survival
                sevent
clus2              0   1
  AGXT MUTATED     5   3
  AGXT WILD-TYPE 310 138
  AGXT MUTATED AGXT WILD-TYPE 
             8            448 
  AGXT MUTATED AGXT WILD-TYPE 
             3            138 
$`AGXT MUTATED`
TCGA-05-4427 TCGA-38-4632 TCGA-44-6779 TCGA-44-7661 TCGA-44-8120 TCGA-55-8507 
       26.01        44.61        16.44        12.03         8.55         0.26 
TCGA-78-7220 TCGA-95-7567 
       26.53        18.67 

$`AGXT WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       14.60        19.46         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64        12.66         3.25        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.36         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
       19.00        17.29         1.12         1.22         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  AGXT MUTATED AGXT WILD-TYPE 
          0.26           0.00 
  AGXT MUTATED AGXT WILD-TYPE 
         44.61         223.96 
  AGXT MUTATED AGXT WILD-TYPE 
        17.555         18.030 
[1] "0.3 - 44.6 (17.6)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D243V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AGXT MUTATED         0        1        2         0         3          1
  AGXT WILD-TYPE       4      122      131        46        64         69
                vv
clus             STAGE IIIB STAGE IV
  AGXT MUTATED            0        1
  AGXT WILD-TYPE         11       24
D243V3, multiclass
            clus
vv           AGXT MUTATED AGXT WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            131
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AGXT MUTATED     1   7   0   0
  AGXT WILD-TYPE 154 254  43  18
D243V4, multiclass
    clus
vv   AGXT MUTATED AGXT WILD-TYPE
  T1            1            154
  T2            7            254
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  AGXT MUTATED     3   4     1
  AGXT WILD-TYPE 304  85    71
D243V5, multiclass
       clus
vv      AGXT MUTATED AGXT WILD-TYPE
  N0               3            304
  N1               4             85
  N2+N3            1             71
[1] 3 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
  AGXT MUTATED     5   1
  AGXT WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AGXT MUTATED      5    1
  AGXT WILD-TYPE  322   22
   clus
vv  AGXT MUTATED AGXT WILD-TYPE
  0            5            322
  1            1             22
[1] 2 2
[1] FALSE
D243V7, binary
                cls
clus               0   1
  AGXT MUTATED     4   4
  AGXT WILD-TYPE 255 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  AGXT MUTATED      4    4
  AGXT WILD-TYPE  255  217
        clus
vv       AGXT MUTATED AGXT WILD-TYPE
  FEMALE            4            255
  MALE              4            217
[1] 2 2
[1] FALSE
D243V8, continuous
[1] "Remove cluster labels:" "AGXT MUTATED"          
clus
  AGXT MUTATED AGXT WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"AGXT WILD-TYPE" "AGXT WILD-TYPE" "AGXT WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AGXT MUTATED                            0                                 3
  AGXT WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AGXT MUTATED                                                    5
  AGXT WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AGXT MUTATED                                            0
  AGXT WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AGXT MUTATED                                               0
  AGXT WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  AGXT MUTATED                                0
  AGXT WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  AGXT MUTATED                                    0
  AGXT WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  AGXT MUTATED                              0                             0
  AGXT WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AGXT MUTATED                                               0
  AGXT WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  AGXT MUTATED                              0
  AGXT WILD-TYPE                            9
D243V9, multiclass
                                                    clus
vv                                                   AGXT MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   AGXT WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V10, binary
                cls
clus               0   1
  AGXT MUTATED     1   7
  AGXT WILD-TYPE  19 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  AGXT MUTATED      1    7
  AGXT WILD-TYPE   19  453
     clus
vv    AGXT MUTATED AGXT WILD-TYPE
  NO             1             19
  YES            7            453
[1] 2 2
[1] FALSE
D243V11, continuous
D243V12, continuous
                vv
clus              R0  R1  R2  RX
  AGXT MUTATED     4   0   0   0
  AGXT WILD-TYPE 306  11   4  25
D243V13, multiclass
    clus
vv   AGXT MUTATED AGXT WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGXT MUTATED                                  0     0
  AGXT WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AGXT MUTATED                           2     5
  AGXT WILD-TYPE                        27   372
D243V14, multiclass
                                  clus
vv                                 AGXT MUTATED AGXT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V15, binary
                cls
clus               0   1
  AGXT MUTATED     0   5
  AGXT WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  AGXT MUTATED      0    5
  AGXT WILD-TYPE    6  344
                        clus
vv                       AGXT MUTATED AGXT WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(244) Variable = PBRM1 MUTATION ANALYSIS
D244V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED     6   2
  PBRM1 WILD-TYPE 309 139
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8             448 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              2             139 
$`PBRM1 MUTATED`
TCGA-05-4382 TCGA-38-4629 TCGA-44-6776 TCGA-44-7659 TCGA-55-7907 TCGA-86-6851 
       19.96        28.41        63.72        14.60         0.53         5.88 
TCGA-86-8672 TCGA-NJ-A55R 
        0.62        19.82 

$`PBRM1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
       29.13         0.26         0.43        59.11 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.53            0.00 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          63.72          223.96 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          17.21           18.03 
[1] "0.5 - 63.7 (17.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1"  
D244V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PBRM1 MUTATED         0        3        1         2         2          0
  PBRM1 WILD-TYPE       4      120      132        44        65         70
                 vv
clus              STAGE IIIB STAGE IV
  PBRM1 MUTATED            0        0
  PBRM1 WILD-TYPE         11       25
D244V3, multiclass
            clus
vv           PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               1             132
  STAGE IIA              2              44
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of 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     4   2   2   0
  PBRM1 WILD-TYPE 151 259  41  18
D244V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1             4             151
  T2             2             259
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PBRM1 MUTATED     6   2     0
  PBRM1 WILD-TYPE 301  87    72
D244V5, multiclass
       clus
vv      PBRM1 MUTATED PBRM1 WILD-TYPE
  N0                6             301
  N1                2              87
  N2+N3             0              72
[1] 3 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
  PBRM1 MUTATED     4   0
  PBRM1 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      4    0
  PBRM1 WILD-TYPE  323   23
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D244V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED     2   6
  PBRM1 WILD-TYPE 257 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      2    6
  PBRM1 WILD-TYPE  257  215
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE             2             257
  MALE               6             215
[1] 2 2
[1] FALSE
D244V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PBRM1 MUTATED                            0                                 2
  PBRM1 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PBRM1 MUTATED                                                    6
  PBRM1 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PBRM1 MUTATED                                            0
  PBRM1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PBRM1 MUTATED                                               0
  PBRM1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PBRM1 MUTATED                                0
  PBRM1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PBRM1 MUTATED                                    0
  PBRM1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PBRM1 MUTATED                              0                             0
  PBRM1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PBRM1 MUTATED                                               0
  PBRM1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PBRM1 MUTATED                              0
  PBRM1 WILD-TYPE                            9
D244V9, multiclass
                                                    clus
vv                                                   PBRM1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PBRM1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V10, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0   8
  PBRM1 WILD-TYPE  20 452
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0    8
  PBRM1 WILD-TYPE   20  452
     clus
vv    PBRM1 MUTATED PBRM1 WILD-TYPE
  NO              0              20
  YES             8             452
[1] 2 2
[1] FALSE
D244V11, continuous
D244V12, continuous
                 vv
clus               R0  R1  R2  RX
  PBRM1 MUTATED     4   0   0   0
  PBRM1 WILD-TYPE 306  11   4  25
D244V13, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PBRM1 MUTATED                                  0     0
  PBRM1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED                           0     7
  PBRM1 WILD-TYPE                        29   370
D244V14, multiclass
                                  clus
vv                                 PBRM1 MUTATED PBRM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V15, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0   6
  PBRM1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0    6
  PBRM1 WILD-TYPE    6  343
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(245) Variable = CREB5 MUTATION ANALYSIS
D245V1, survival
                 sevent
clus2               0   1
  CREB5 MUTATED     8   5
  CREB5 WILD-TYPE 307 136
  CREB5 MUTATED CREB5 WILD-TYPE 
             13             443 
  CREB5 MUTATED CREB5 WILD-TYPE 
              5             136 
$`CREB5 MUTATED`
TCGA-38-7271 TCGA-49-4506 TCGA-55-6712 TCGA-55-7907 TCGA-55-8096 TCGA-55-8511 
       26.30        32.84         0.79         0.53        23.64         0.30 
TCGA-55-A490 TCGA-67-3771 TCGA-78-7155 TCGA-97-A4M0 TCGA-99-8028 TCGA-MP-A4T4 
        1.58        20.05        38.50        21.44        36.76        86.04 
TCGA-NJ-A4YP 
        1.64 

$`CREB5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       44.61        14.73         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        46.72        14.07         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06         0.13        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  CREB5 MUTATED CREB5 WILD-TYPE 
            0.3             0.0 
  CREB5 MUTATED CREB5 WILD-TYPE 
          86.04          223.96 
  CREB5 MUTATED CREB5 WILD-TYPE 
          21.44           17.92 
[1] "0.3 - 86.0 (21.4)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.3"
D245V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CREB5 MUTATED         0        3        5         3         2          0
  CREB5 WILD-TYPE       4      120      128        43        65         70
                 vv
clus              STAGE IIIB STAGE IV
  CREB5 MUTATED            0        0
  CREB5 WILD-TYPE         11       25
D245V3, multiclass
            clus
vv           CREB5 MUTATED CREB5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               5             128
  STAGE IIA              3              43
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CREB5 MUTATED     3  10   0   0
  CREB5 WILD-TYPE 152 251  43  18
D245V4, multiclass
    clus
vv   CREB5 MUTATED CREB5 WILD-TYPE
  T1             3             152
  T2            10             251
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  CREB5 MUTATED     9   4     0
  CREB5 WILD-TYPE 298  85    72
D245V5, multiclass
       clus
vv      CREB5 MUTATED CREB5 WILD-TYPE
  N0                9             298
  N1                4              85
  N2+N3             0              72
[1] 3 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
  CREB5 MUTATED     8   0
  CREB5 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREB5 MUTATED      8    0
  CREB5 WILD-TYPE  319   23
   clus
vv  CREB5 MUTATED CREB5 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D245V7, binary
                 cls
clus                0   1
  CREB5 MUTATED     8   5
  CREB5 WILD-TYPE 251 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREB5 MUTATED      8    5
  CREB5 WILD-TYPE  251  216
        clus
vv       CREB5 MUTATED CREB5 WILD-TYPE
  FEMALE             8             251
  MALE               5             216
[1] 2 2
[1] FALSE
D245V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CREB5 MUTATED                            0                                 1
  CREB5 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CREB5 MUTATED                                                   11
  CREB5 WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CREB5 MUTATED                                            0
  CREB5 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CREB5 MUTATED                                               0
  CREB5 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CREB5 MUTATED                                0
  CREB5 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CREB5 MUTATED                                    0
  CREB5 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CREB5 MUTATED                              0                             1
  CREB5 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CREB5 MUTATED                                               0
  CREB5 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CREB5 MUTATED                              0
  CREB5 WILD-TYPE                            9
D245V9, multiclass
                                                    clus
vv                                                   CREB5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CREB5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V10, binary
                 cls
clus                0   1
  CREB5 MUTATED     0  13
  CREB5 WILD-TYPE  20 447
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREB5 MUTATED      0   13
  CREB5 WILD-TYPE   20  447
     clus
vv    CREB5 MUTATED CREB5 WILD-TYPE
  NO              0              20
  YES            13             447
[1] 2 2
[1] FALSE
D245V11, continuous
D245V12, continuous
                 vv
clus               R0  R1  R2  RX
  CREB5 MUTATED     8   1   0   0
  CREB5 WILD-TYPE 302  10   4  25
D245V13, multiclass
    clus
vv   CREB5 MUTATED CREB5 WILD-TYPE
  R0             8             302
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREB5 MUTATED                                  0     0
  CREB5 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CREB5 MUTATED                           2    11
  CREB5 WILD-TYPE                        27   366
D245V14, multiclass
                                  clus
vv                                 CREB5 MUTATED CREB5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V15, binary
                 cls
clus                0   1
  CREB5 MUTATED     0  10
  CREB5 WILD-TYPE   6 339
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREB5 MUTATED      0   10
  CREB5 WILD-TYPE    6  339
                        clus
vv                       CREB5 MUTATED CREB5 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            10             339
[1] 2 2
[1] FALSE

Clustering(246) Variable = CD300E MUTATION ANALYSIS
D246V1, survival
                  sevent
clus2                0   1
  CD300E MUTATED     6   1
  CD300E WILD-TYPE 309 140
  CD300E MUTATED CD300E WILD-TYPE 
               7              449 
  CD300E MUTATED CD300E WILD-TYPE 
               1              140 
$`CD300E MUTATED`
TCGA-44-7669 TCGA-55-6985 TCGA-55-7907 TCGA-69-7978 TCGA-69-7980 TCGA-78-7539 
       18.87        40.54         0.53         2.30        12.56        10.75 
TCGA-83-5908 
       27.09 

$`CD300E WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       32.71        60.03        24.99       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78         1.45        18.64         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  CD300E MUTATED CD300E WILD-TYPE 
            0.53             0.00 
  CD300E MUTATED CD300E WILD-TYPE 
           40.54           223.96 
  CD300E MUTATED CD300E WILD-TYPE 
           12.56            18.08 
[1] "0.5 - 40.5 (12.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D246V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CD300E MUTATED         1        1        1         3         1          0
  CD300E WILD-TYPE       3      122      132        43        66         70
                  vv
clus               STAGE IIIB STAGE IV
  CD300E MUTATED            0        0
  CD300E WILD-TYPE         11       25
D246V3, multiclass
            clus
vv           CD300E MUTATED CD300E WILD-TYPE
  STAGE I                 1                3
  STAGE IA                1              122
  STAGE IB                1              132
  STAGE IIA               3               43
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CD300E MUTATED     3   4   0   0
  CD300E WILD-TYPE 152 257  43  18
D246V4, multiclass
    clus
vv   CD300E MUTATED CD300E WILD-TYPE
  T1              3              152
  T2              4              257
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  CD300E MUTATED     4   3     0
  CD300E WILD-TYPE 303  86    72
D246V5, multiclass
       clus
vv      CD300E MUTATED CD300E WILD-TYPE
  N0                 4              303
  N1                 3               86
  N2+N3              0               72
[1] 3 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
  CD300E MUTATED     3   0
  CD300E WILD-TYPE 324  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      3    0
  CD300E WILD-TYPE  324   23
   clus
vv  CD300E MUTATED CD300E WILD-TYPE
  0              3              324
  1              0               23
[1] 2 2
[1] FALSE
D246V7, binary
                  cls
clus                 0   1
  CD300E MUTATED     4   3
  CD300E WILD-TYPE 255 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      4    3
  CD300E WILD-TYPE  255  218
        clus
vv       CD300E MUTATED CD300E WILD-TYPE
  FEMALE              4              255
  MALE                3              218
[1] 2 2
[1] FALSE
D246V8, continuous
[1] "Remove cluster labels:" "CD300E MUTATED"        
clus
  CD300E MUTATED CD300E WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-75-5122       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"CD300E WILD-TYPE" "CD300E WILD-TYPE" "CD300E WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CD300E MUTATED                            0                                 2
  CD300E WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CD300E MUTATED                                                    5
  CD300E WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CD300E MUTATED                                            0
  CD300E WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CD300E MUTATED                                               0
  CD300E WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CD300E MUTATED                                0
  CD300E WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CD300E MUTATED                                    0
  CD300E WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CD300E MUTATED                              0                             0
  CD300E WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CD300E MUTATED                                               0
  CD300E WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CD300E MUTATED                              0
  CD300E WILD-TYPE                            9
D246V9, multiclass
                                                    clus
vv                                                   CD300E MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CD300E WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V10, binary
                  cls
clus                 0   1
  CD300E MUTATED     0   7
  CD300E WILD-TYPE  20 453
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      0    7
  CD300E WILD-TYPE   20  453
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               0               20
  YES              7              453
[1] 2 2
[1] FALSE
D246V11, continuous
D246V12, continuous
                  vv
clus                R0  R1  R2  RX
  CD300E MUTATED     4   0   0   0
  CD300E WILD-TYPE 306  11   4  25
D246V13, multiclass
    clus
vv   CD300E MUTATED CD300E WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD300E MUTATED                                  0     0
  CD300E WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CD300E MUTATED                           1     6
  CD300E WILD-TYPE                        28   371
D246V14, multiclass
                                  clus
vv                                 CD300E MUTATED CD300E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         6              371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V15, binary
                  cls
clus                 0   1
  CD300E MUTATED     0   5
  CD300E WILD-TYPE   6 344
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      0    5
  CD300E WILD-TYPE    6  344
                        clus
vv                       CD300E MUTATED CD300E WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              344
[1] 2 2
[1] FALSE

Clustering(247) Variable = ZNF623 MUTATION ANALYSIS
D247V1, survival
                  sevent
clus2                0   1
  ZNF623 MUTATED     3   5
  ZNF623 WILD-TYPE 312 136
  ZNF623 MUTATED ZNF623 WILD-TYPE 
               8              448 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
               5              136 
$`ZNF623 MUTATED`
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-35-5375 TCGA-55-1592 TCGA-55-6712 
        0.00         9.96        24.03         8.68        23.05         0.79 
TCGA-78-7536 TCGA-91-A4BC 
        8.02         1.45 

$`ZNF623 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        5.98        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 
       27.25        34.29        30.54        13.94         9.21        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07        32.65        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        1.15        16.18        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ZNF623 MUTATED ZNF623 WILD-TYPE 
            0.00             0.07 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
           24.03           223.96 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
            8.35            18.15 
[1] "0.0 - 24.0 (8.3)"   "0.1 - 224.0 (18.1)"
[1] "hr=" "6.3"
D247V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF623 MUTATED         0        1        1         2         1          2
  ZNF623 WILD-TYPE       4      122      132        44        66         68
                  vv
clus               STAGE IIIB STAGE IV
  ZNF623 MUTATED            2        0
  ZNF623 WILD-TYPE          9       25
D247V3, multiclass
            clus
vv           ZNF623 MUTATED ZNF623 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                1              132
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              2                9
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF623 MUTATED     0   7   0   2
  ZNF623 WILD-TYPE 155 254  43  16
D247V4, multiclass
    clus
vv   ZNF623 MUTATED ZNF623 WILD-TYPE
  T1              0              155
  T2              7              254
  T3              0               43
  T4              2               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"
                  vv
clus                N0  N1 N2+N3
  ZNF623 MUTATED     3   3     3
  ZNF623 WILD-TYPE 304  86    69
D247V5, multiclass
       clus
vv      ZNF623 MUTATED ZNF623 WILD-TYPE
  N0                 3              304
  N1                 3               86
  N2+N3              3               69
[1] 3 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
  ZNF623 MUTATED     7   0
  ZNF623 WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      7    0
  ZNF623 WILD-TYPE  320   23
   clus
vv  ZNF623 MUTATED ZNF623 WILD-TYPE
  0              7              320
  1              0               23
[1] 2 2
[1] FALSE
D247V7, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     1   8
  ZNF623 WILD-TYPE 258 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      1    8
  ZNF623 WILD-TYPE  258  213
        clus
vv       ZNF623 MUTATED ZNF623 WILD-TYPE
  FEMALE              1              258
  MALE                8              213
[1] 2 2
[1] FALSE
D247V8, continuous
[1] "Remove cluster labels:" "ZNF623 MUTATED"        
clus
  ZNF623 MUTATED ZNF623 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-53-A4EZ       TCGA-55-7283 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-55-7573       TCGA-55-7725       TCGA-55-7910       TCGA-55-7914 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-55-8089       TCGA-55-8096       TCGA-55-8205       TCGA-55-8208 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" "ZNF623 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF623 MUTATED                            0                                 3
  ZNF623 WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF623 MUTATED                                                    6
  ZNF623 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF623 MUTATED                                            0
  ZNF623 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF623 MUTATED                                               0
  ZNF623 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF623 MUTATED                                0
  ZNF623 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF623 MUTATED                                    0
  ZNF623 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF623 MUTATED                              0                             0
  ZNF623 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF623 MUTATED                                               0
  ZNF623 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF623 MUTATED                              0
  ZNF623 WILD-TYPE                            9
D247V9, multiclass
                                                    clus
vv                                                   ZNF623 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF623 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V10, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     1   8
  ZNF623 WILD-TYPE  19 452
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      1    8
  ZNF623 WILD-TYPE   19  452
     clus
vv    ZNF623 MUTATED ZNF623 WILD-TYPE
  NO               1               19
  YES              8              452
[1] 2 2
[1] FALSE
D247V11, continuous
D247V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF623 MUTATED     7   0   0   0
  ZNF623 WILD-TYPE 303  11   4  25
D247V13, multiclass
    clus
vv   ZNF623 MUTATED ZNF623 WILD-TYPE
  R0              7              303
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF623 MUTATED                                  0     0
  ZNF623 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF623 MUTATED                           0     5
  ZNF623 WILD-TYPE                        29   372
D247V14, multiclass
                                  clus
vv                                 ZNF623 MUTATED ZNF623 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V15, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     0   3
  ZNF623 WILD-TYPE   6 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      0    3
  ZNF623 WILD-TYPE    6  346
                        clus
vv                       ZNF623 MUTATED ZNF623 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              3              346
[1] 2 2
[1] FALSE

Clustering(248) Variable = CYSLTR2 MUTATION ANALYSIS
D248V1, survival
                   sevent
clus2                 0   1
  CYSLTR2 MUTATED     5   4
  CYSLTR2 WILD-TYPE 310 137
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                9               447 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                4               137 
$`CYSLTR2 MUTATED`
TCGA-50-5045 TCGA-55-8620 TCGA-62-A46O TCGA-73-4677 TCGA-86-8585 TCGA-91-6848 
       71.47         2.17        47.80         1.25         1.15         7.36 
TCGA-95-7039 TCGA-MN-A4N4 TCGA-MP-A4T2 
        1.12        38.63        37.35 

$`CYSLTR2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 
       29.26        17.16        11.64        22.26        20.52        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.58         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         1.32         5.39        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        58.45        49.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
             1.12              0.00 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            71.47            223.96 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
             7.36             18.08 
[1] "1.1 - 71.5 (7.4)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D248V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CYSLTR2 MUTATED         0        4        2         0         1          1
  CYSLTR2 WILD-TYPE       4      119      131        46        66         69
                   vv
clus                STAGE IIIB STAGE IV
  CYSLTR2 MUTATED            0        1
  CYSLTR2 WILD-TYPE         11       24
D248V3, multiclass
            clus
vv           CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 4               119
  STAGE IB                 2               131
  STAGE IIA                0                46
  STAGE IIB                1                66
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYSLTR2 MUTATED     3   5   1   0
  CYSLTR2 WILD-TYPE 152 256  42  18
D248V4, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  T1               3               152
  T2               5               256
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  CYSLTR2 MUTATED     6   2     1
  CYSLTR2 WILD-TYPE 301  87    71
D248V5, multiclass
       clus
vv      CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  N0                  6               301
  N1                  2                87
  N2+N3               1                71
[1] 3 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
  CYSLTR2 MUTATED     6   1
  CYSLTR2 WILD-TYPE 321  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      6    1
  CYSLTR2 WILD-TYPE  321   22
   clus
vv  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  0               6               321
  1               1                22
[1] 2 2
[1] FALSE
D248V7, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED     3   6
  CYSLTR2 WILD-TYPE 256 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      3    6
  CYSLTR2 WILD-TYPE  256  215
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  FEMALE               3               256
  MALE                 6               215
[1] 2 2
[1] FALSE
D248V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  CYSLTR2 MUTATED                            0
  CYSLTR2 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  CYSLTR2 MUTATED                                   1
  CYSLTR2 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CYSLTR2 MUTATED                                                    7
  CYSLTR2 WILD-TYPE                                                287
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CYSLTR2 MUTATED                                            0
  CYSLTR2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CYSLTR2 MUTATED                                               0
  CYSLTR2 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  CYSLTR2 MUTATED                                0
  CYSLTR2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  CYSLTR2 MUTATED                                    0
  CYSLTR2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CYSLTR2 MUTATED                              0                             0
  CYSLTR2 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CYSLTR2 MUTATED                                               1
  CYSLTR2 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  CYSLTR2 MUTATED                              0
  CYSLTR2 WILD-TYPE                            9
D248V9, multiclass
                                                    clus
vv                                                   CYSLTR2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   CYSLTR2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V10, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED     1   8
  CYSLTR2 WILD-TYPE  19 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      1    8
  CYSLTR2 WILD-TYPE   19  452
     clus
vv    CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  NO                1                19
  YES               8               452
[1] 2 2
[1] FALSE
D248V11, continuous
D248V12, continuous
                   vv
clus                 R0  R1  R2  RX
  CYSLTR2 MUTATED     6   0   0   0
  CYSLTR2 WILD-TYPE 304  11   4  25
D248V13, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYSLTR2 MUTATED                                  0     0
  CYSLTR2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYSLTR2 MUTATED                           1     8
  CYSLTR2 WILD-TYPE                        28   369
D248V14, multiclass
                                  clus
vv                                 CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          8               369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V15, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED     0   9
  CYSLTR2 WILD-TYPE   6 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      0    9
  CYSLTR2 WILD-TYPE    6  340
                        clus
vv                       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               9               340
[1] 2 2
[1] FALSE

Clustering(249) Variable = BCL9L MUTATION ANALYSIS
D249V1, survival
                 sevent
clus2               0   1
  BCL9L MUTATED    13   3
  BCL9L WILD-TYPE 302 138
  BCL9L MUTATED BCL9L WILD-TYPE 
             16             440 
  BCL9L MUTATED BCL9L WILD-TYPE 
              3             138 
$`BCL9L MUTATED`
TCGA-05-4397 TCGA-35-4122 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-8119 
       24.03         7.40        23.18        63.72        32.45         3.25 
TCGA-55-6543 TCGA-55-7903 TCGA-55-8094 TCGA-64-5781 TCGA-69-8254 TCGA-78-7166 
        0.07        18.64         0.13        51.25        13.45         8.48 
TCGA-91-6848 TCGA-91-A4BC TCGA-95-7043 TCGA-97-8547 
        7.36         1.45         1.22        21.60 

$`BCL9L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.15        21.63        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         5.06        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       12.56        14.01         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.29         7.07       104.19       223.96        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        1.15        16.18        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        14.30        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  BCL9L MUTATED BCL9L WILD-TYPE 
           0.07            0.00 
  BCL9L MUTATED BCL9L WILD-TYPE 
          63.72          223.96 
  BCL9L MUTATED BCL9L WILD-TYPE 
         10.965          18.100 
[1] "0.1 - 63.7 (11.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D249V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BCL9L MUTATED         0        5        3         1         3          3
  BCL9L WILD-TYPE       4      118      130        45        64         67
                 vv
clus              STAGE IIIB STAGE IV
  BCL9L MUTATED            0        1
  BCL9L WILD-TYPE         11       24
D249V3, multiclass
            clus
vv           BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               3             130
  STAGE IIA              1              45
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of 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     5  11   1   0
  BCL9L WILD-TYPE 150 250  42  18
D249V4, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  T1             5             150
  T2            11             250
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  BCL9L MUTATED    10   2     3
  BCL9L WILD-TYPE 297  87    69
D249V5, multiclass
       clus
vv      BCL9L MUTATED BCL9L WILD-TYPE
  N0               10             297
  N1                2              87
  N2+N3             3              69
[1] 3 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
  BCL9L MUTATED     6   1
  BCL9L WILD-TYPE 321  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      6    1
  BCL9L WILD-TYPE  321   22
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0             6             321
  1             1              22
[1] 2 2
[1] FALSE
D249V7, binary
                 cls
clus                0   1
  BCL9L MUTATED     8   9
  BCL9L WILD-TYPE 251 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      8    9
  BCL9L WILD-TYPE  251  212
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  FEMALE             8             251
  MALE               9             212
[1] 2 2
[1] FALSE
D249V8, continuous
[1] "Remove cluster labels:" "BCL9L MUTATED"         
clus
  BCL9L MUTATED BCL9L WILD-TYPE 
              2              82 
     TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ      TCGA-55-7283 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-69-7974      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BCL9L MUTATED                            0                                 5
  BCL9L WILD-TYPE                         18                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BCL9L MUTATED                                                   11
  BCL9L WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BCL9L MUTATED                                            1
  BCL9L WILD-TYPE                                          3
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BCL9L MUTATED                                               0
  BCL9L WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  BCL9L MUTATED                                0
  BCL9L WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  BCL9L MUTATED                                    0
  BCL9L WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BCL9L MUTATED                              0                             0
  BCL9L WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BCL9L MUTATED                                               0
  BCL9L WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  BCL9L MUTATED                              0
  BCL9L WILD-TYPE                            9
D249V9, multiclass
                                                    clus
vv                                                   BCL9L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   BCL9L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V10, binary
                 cls
clus                0   1
  BCL9L MUTATED     2  15
  BCL9L WILD-TYPE  18 445
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      2   15
  BCL9L WILD-TYPE   18  445
     clus
vv    BCL9L MUTATED BCL9L WILD-TYPE
  NO              2              18
  YES            15             445
[1] 2 2
[1] FALSE
D249V11, continuous
D249V12, continuous
                 vv
clus               R0  R1  R2  RX
  BCL9L MUTATED     7   0   0   1
  BCL9L WILD-TYPE 303  11   4  24
D249V13, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCL9L MUTATED                                  0     0
  BCL9L WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BCL9L MUTATED                           0    14
  BCL9L WILD-TYPE                        29   363
D249V14, multiclass
                                  clus
vv                                 BCL9L MUTATED BCL9L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V15, binary
                 cls
clus                0   1
  BCL9L MUTATED     1   9
  BCL9L WILD-TYPE   5 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      1    9
  BCL9L WILD-TYPE    5  340
                        clus
vv                       BCL9L MUTATED BCL9L WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(250) Variable = ZFP36L1 MUTATION ANALYSIS
D250V1, survival
                   sevent
clus2                 0   1
  ZFP36L1 MUTATED     8   3
  ZFP36L1 WILD-TYPE 307 138
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               11               445 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                3               138 
$`ZFP36L1 MUTATED`
TCGA-05-4249 TCGA-38-7271 TCGA-44-5643 TCGA-55-6712 TCGA-55-7994 TCGA-55-8089 
       50.07        26.30        33.30         0.79        19.82         3.29 
TCGA-69-8254 TCGA-73-7498 TCGA-78-7159 TCGA-78-7167 TCGA-NJ-A4YI 
       13.45        39.09        64.90        88.14         0.13 

$`ZFP36L1 WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       37.15        38.24        34.06         6.25        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       23.05        48.62         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
       18.64         0.53         6.48        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1.25        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      223.96         8.48        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
             0.13              0.00 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            88.14            223.96 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            26.30             17.92 
[1] "0.1 - 88.1 (26.3)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.7"
D250V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZFP36L1 MUTATED         0        4        1         1         1          2
  ZFP36L1 WILD-TYPE       4      119      132        45        66         68
                   vv
clus                STAGE IIIB STAGE IV
  ZFP36L1 MUTATED            0        1
  ZFP36L1 WILD-TYPE         11       24
D250V3, multiclass
            clus
vv           ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 4               119
  STAGE IB                 1               132
  STAGE IIA                1                45
  STAGE IIB                1                66
  STAGE IIIA               2                68
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of 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     4   6   1   0
  ZFP36L1 WILD-TYPE 151 255  42  18
D250V4, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  T1               4               151
  T2               6               255
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  ZFP36L1 MUTATED     6   1     2
  ZFP36L1 WILD-TYPE 301  88    70
D250V5, multiclass
       clus
vv      ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  N0                  6               301
  N1                  1                88
  N2+N3               2                70
[1] 3 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
  ZFP36L1 MUTATED     7   1
  ZFP36L1 WILD-TYPE 320  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      7    1
  ZFP36L1 WILD-TYPE  320   22
   clus
vv  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  0               7               320
  1               1                22
[1] 2 2
[1] FALSE
D250V7, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     4   7
  ZFP36L1 WILD-TYPE 255 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      4    7
  ZFP36L1 WILD-TYPE  255  214
        clus
vv       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  FEMALE               4               255
  MALE                 7               214
[1] 2 2
[1] FALSE
D250V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ZFP36L1 MUTATED                            0
  ZFP36L1 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZFP36L1 MUTATED                                   2
  ZFP36L1 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZFP36L1 MUTATED                                                    6
  ZFP36L1 WILD-TYPE                                                288
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZFP36L1 MUTATED                                            0
  ZFP36L1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZFP36L1 MUTATED                                               1
  ZFP36L1 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ZFP36L1 MUTATED                                0
  ZFP36L1 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ZFP36L1 MUTATED                                    0
  ZFP36L1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZFP36L1 MUTATED                              0                             2
  ZFP36L1 WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZFP36L1 MUTATED                                               0
  ZFP36L1 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ZFP36L1 MUTATED                              0
  ZFP36L1 WILD-TYPE                            9
D250V9, multiclass
                                                    clus
vv                                                   ZFP36L1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ZFP36L1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V10, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     1  10
  ZFP36L1 WILD-TYPE  19 450
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      1   10
  ZFP36L1 WILD-TYPE   19  450
     clus
vv    ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  NO                1                19
  YES              10               450
[1] 2 2
[1] FALSE
D250V11, continuous
D250V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ZFP36L1 MUTATED     7   0   0   0
  ZFP36L1 WILD-TYPE 303  11   4  25
D250V13, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  R0               7               303
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP36L1 MUTATED                                  0     0
  ZFP36L1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L1 MUTATED                           1     9
  ZFP36L1 WILD-TYPE                        28   368
D250V14, multiclass
                                  clus
vv                                 ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          9               368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V15, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     0   6
  ZFP36L1 WILD-TYPE   6 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      0    6
  ZFP36L1 WILD-TYPE    6  343
                        clus
vv                       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               6               343
[1] 2 2
[1] FALSE

Clustering(251) Variable = PALM MUTATION ANALYSIS
D251V1, survival
                sevent
clus2              0   1
  PALM MUTATED     5   1
  PALM WILD-TYPE 310 140
  PALM MUTATED PALM WILD-TYPE 
             6            450 
  PALM MUTATED PALM WILD-TYPE 
             1            140 
$`PALM MUTATED`
TCGA-44-8117 TCGA-49-4506 TCGA-55-8302 TCGA-62-8399 TCGA-69-7973 TCGA-95-7039 
       12.66        32.84         0.76        88.64         7.56         1.12 

$`PALM WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        46.72        14.07         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  PALM MUTATED PALM WILD-TYPE 
          0.76           0.00 
  PALM MUTATED PALM WILD-TYPE 
         88.64         223.96 
  PALM MUTATED PALM WILD-TYPE 
         10.11          18.10 
[1] "0.8 - 88.6 (10.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.2"
D251V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PALM MUTATED         0        0        3         0         2          1
  PALM WILD-TYPE       4      123      130        46        65         69
                vv
clus             STAGE IIIB STAGE IV
  PALM MUTATED            0        0
  PALM WILD-TYPE         11       25
D251V3, multiclass
            clus
vv           PALM MUTATED PALM WILD-TYPE
  STAGE I               0              4
  STAGE IA              0            123
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             2             65
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PALM MUTATED     0   5   1   0
  PALM WILD-TYPE 155 256  42  18
D251V4, multiclass
    clus
vv   PALM MUTATED PALM WILD-TYPE
  T1            0            155
  T2            5            256
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  PALM MUTATED     4   1     1
  PALM WILD-TYPE 303  88    71
D251V5, multiclass
       clus
vv      PALM MUTATED PALM WILD-TYPE
  N0               4            303
  N1               1             88
  N2+N3            1             71
[1] 3 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
  PALM MUTATED     4   0
  PALM WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  PALM MUTATED      4    0
  PALM WILD-TYPE  323   23
   clus
vv  PALM MUTATED PALM WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D251V7, binary
                cls
clus               0   1
  PALM MUTATED     4   2
  PALM WILD-TYPE 255 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  PALM MUTATED      4    2
  PALM WILD-TYPE  255  219
        clus
vv       PALM MUTATED PALM WILD-TYPE
  FEMALE            4            255
  MALE              2            219
[1] 2 2
[1] FALSE
D251V8, continuous
[1] "Remove cluster labels:" "PALM MUTATED"          
clus
  PALM MUTATED PALM WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8402     TCGA-62-A46O 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PALM MUTATED                            0                                 2
  PALM WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PALM MUTATED                                                    3
  PALM WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PALM MUTATED                                            0
  PALM WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PALM MUTATED                                               0
  PALM WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  PALM MUTATED                                0
  PALM WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  PALM MUTATED                                    0
  PALM WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PALM MUTATED                              0                             1
  PALM WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PALM MUTATED                                               0
  PALM WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  PALM MUTATED                              0
  PALM WILD-TYPE                            9
D251V9, multiclass
                                                    clus
vv                                                   PALM MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   PALM WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V10, binary
                cls
clus               0   1
  PALM MUTATED     0   6
  PALM WILD-TYPE  20 454
[1] "tbl2"
                cls
clus             [,1] [,2]
  PALM MUTATED      0    6
  PALM WILD-TYPE   20  454
     clus
vv    PALM MUTATED PALM WILD-TYPE
  NO             0             20
  YES            6            454
[1] 2 2
[1] FALSE
D251V11, continuous
D251V12, continuous
[1] "Remove cluster labels:" "PALM MUTATED"          
clus
  PALM MUTATED PALM WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     TCGA-44-3396 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-5644 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6147 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     TCGA-44-6776 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7661     TCGA-44-7662     TCGA-44-7667 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7670     TCGA-44-7672     TCGA-44-8119 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4494     TCGA-49-4505     TCGA-53-7624 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-1592 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-1595     TCGA-55-5899     TCGA-55-6642     TCGA-55-6712 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-6971     TCGA-55-7227     TCGA-55-7283     TCGA-55-7570 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7728     TCGA-55-7907     TCGA-55-7910 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7914     TCGA-55-8089     TCGA-55-8092 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8205 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8506     TCGA-55-8507 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8514     TCGA-55-8615 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-62-8398     TCGA-64-1677 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5774     TCGA-64-5775     TCGA-64-5778 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-64-5779     TCGA-64-5781     TCGA-69-7761     TCGA-69-7763 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-69-7764     TCGA-69-7765     TCGA-69-7974     TCGA-69-7979 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K     TCGA-73-4659 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-7498     TCGA-75-6214 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-75-7025     TCGA-75-7027     TCGA-75-7031     TCGA-78-7145 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7542 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6851     TCGA-86-7711     TCGA-86-7714 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-7954     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6836 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"PALM WILD-TYPE" "PALM WILD-TYPE" "PALM WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  PALM MUTATED     2   1   0   0
  PALM WILD-TYPE 308  10   4  25
D251V13, multiclass
    clus
vv   PALM MUTATED PALM WILD-TYPE
  R0            2            308
  R1            1             10
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PALM MUTATED                                  0     0
  PALM WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PALM MUTATED                           0     6
  PALM WILD-TYPE                        29   371
D251V14, multiclass
                                  clus
vv                                 PALM MUTATED PALM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       6            371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V15, binary
                cls
clus               0   1
  PALM MUTATED     0   5
  PALM WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  PALM MUTATED      0    5
  PALM WILD-TYPE    6  344
                        clus
vv                       PALM MUTATED PALM WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(252) Variable = CSNK1A1L MUTATION ANALYSIS
D252V1, survival
                    sevent
clus2                  0   1
  CSNK1A1L MUTATED    10   3
  CSNK1A1L WILD-TYPE 305 138
  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE 
                13                443 
  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE 
                 3                138 
$`CSNK1A1L MUTATED`
TCGA-05-4415 TCGA-35-5375 TCGA-44-8117 TCGA-44-8120 TCGA-49-4487 TCGA-62-A46O 
        2.99         8.68        12.66         8.55        28.11        47.80 
TCGA-69-7974 TCGA-73-4666 TCGA-78-7633 TCGA-86-7701 TCGA-86-7954 TCGA-95-7039 
        6.05        26.30        32.68        31.13        19.89         1.12 
TCGA-99-8028 
       36.76 

$`CSNK1A1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
       18.87        29.00        17.59        23.64         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       76.21        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       29.98        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        10.75        39.35        10.55       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
        5.88        34.39        13.87        20.55        19.43        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE 
              1.12               0.00 
  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE 
             47.80             223.96 
  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE 
             19.89              17.98 
[1] "1.1 - 47.8 (19.9)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D252V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CSNK1A1L MUTATED         0        3        4         0         1          2
  CSNK1A1L WILD-TYPE       4      120      129        46        66         68
                    vv
clus                 STAGE IIIB STAGE IV
  CSNK1A1L MUTATED            1        2
  CSNK1A1L WILD-TYPE         10       23
D252V3, multiclass
            clus
vv           CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  3                120
  STAGE IB                  4                129
  STAGE IIA                 0                 46
  STAGE IIB                 1                 66
  STAGE IIIA                2                 68
  STAGE IIIB                1                 10
  STAGE IV                  2                 23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CSNK1A1L MUTATED     3   8   1   1
  CSNK1A1L WILD-TYPE 152 253  42  17
D252V4, multiclass
    clus
vv   CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  T1                3                152
  T2                8                253
  T3                1                 42
  T4                1                 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"
                    vv
clus                  N0  N1 N2+N3
  CSNK1A1L MUTATED    10   0     3
  CSNK1A1L WILD-TYPE 297  89    69
D252V5, multiclass
       clus
vv      CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  N0                  10                297
  N1                   0                 89
  N2+N3                3                 69
[1] 3 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
  CSNK1A1L MUTATED     9   2
  CSNK1A1L WILD-TYPE 318  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CSNK1A1L MUTATED      9    2
  CSNK1A1L WILD-TYPE  318   21
   clus
vv  CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  0                9                318
  1                2                 21
[1] 2 2
[1] FALSE
D252V7, binary
                    cls
clus                   0   1
  CSNK1A1L MUTATED     8   5
  CSNK1A1L WILD-TYPE 251 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CSNK1A1L MUTATED      8    5
  CSNK1A1L WILD-TYPE  251  216
        clus
vv       CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  FEMALE                8                251
  MALE                  5                216
[1] 2 2
[1] FALSE
D252V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  CSNK1A1L MUTATED                            0
  CSNK1A1L WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  CSNK1A1L MUTATED                                   4
  CSNK1A1L WILD-TYPE                                98
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CSNK1A1L MUTATED                                                    8
  CSNK1A1L WILD-TYPE                                                286
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CSNK1A1L MUTATED                                            0
  CSNK1A1L WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CSNK1A1L MUTATED                                               1
  CSNK1A1L WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  CSNK1A1L MUTATED                                0
  CSNK1A1L WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  CSNK1A1L MUTATED                                    0
  CSNK1A1L WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CSNK1A1L MUTATED                              0                             0
  CSNK1A1L WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CSNK1A1L MUTATED                                               0
  CSNK1A1L WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  CSNK1A1L MUTATED                              0
  CSNK1A1L WILD-TYPE                            9
D252V9, multiclass
                                                    clus
vv                                                   CSNK1A1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   CSNK1A1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V10, binary
                    cls
clus                   0   1
  CSNK1A1L MUTATED     2  11
  CSNK1A1L WILD-TYPE  18 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CSNK1A1L MUTATED      2   11
  CSNK1A1L WILD-TYPE   18  449
     clus
vv    CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  NO                 2                 18
  YES               11                449
[1] 2 2
[1] FALSE
D252V11, continuous
D252V12, continuous
                    vv
clus                  R0  R1  R2  RX
  CSNK1A1L MUTATED     9   0   0   0
  CSNK1A1L WILD-TYPE 301  11   4  25
D252V13, multiclass
    clus
vv   CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  R0                9                301
  R1                0                 11
  R2                0                  4
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK1A1L MUTATED                                  0     0
  CSNK1A1L WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CSNK1A1L MUTATED                           2    10
  CSNK1A1L WILD-TYPE                        27   367
D252V14, multiclass
                                  clus
vv                                 CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       2                 27
  WHITE                                          10                367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V15, binary
                    cls
clus                   0   1
  CSNK1A1L MUTATED     0  11
  CSNK1A1L WILD-TYPE   6 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CSNK1A1L MUTATED      0   11
  CSNK1A1L WILD-TYPE    6  338
                        clus
vv                       CSNK1A1L MUTATED CSNK1A1L WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               11                338
[1] 2 2
[1] FALSE

Clustering(253) Variable = SCML4 MUTATION ANALYSIS
D253V1, survival
                 sevent
clus2               0   1
  SCML4 MUTATED     7   2
  SCML4 WILD-TYPE 308 139
  SCML4 MUTATED SCML4 WILD-TYPE 
              9             447 
  SCML4 MUTATED SCML4 WILD-TYPE 
              2             139 
$`SCML4 MUTATED`
TCGA-05-4389 TCGA-50-5933 TCGA-55-6985 TCGA-62-8399 TCGA-69-7980 TCGA-91-6836 
       45.01        78.67        40.54        88.64        12.56        13.71 
TCGA-91-7771 TCGA-95-7039 TCGA-J2-A4AD 
       16.18         1.12        18.08 

$`SCML4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       60.03        24.99       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        7.36         1.15        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        23.80        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SCML4 MUTATED SCML4 WILD-TYPE 
           1.12            0.00 
  SCML4 MUTATED SCML4 WILD-TYPE 
          88.64          223.96 
  SCML4 MUTATED SCML4 WILD-TYPE 
          18.08           17.98 
[1] "1.1 - 88.6 (18.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.4"
D253V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SCML4 MUTATED         1        2        2         1         2          2
  SCML4 WILD-TYPE       3      121      131        45        65         68
                 vv
clus              STAGE IIIB STAGE IV
  SCML4 MUTATED            1        0
  SCML4 WILD-TYPE         10       25
D253V3, multiclass
            clus
vv           SCML4 MUTATED SCML4 WILD-TYPE
  STAGE I                1               3
  STAGE IA               2             121
  STAGE IB               2             131
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             2              68
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCML4 MUTATED     3   4   3   1
  SCML4 WILD-TYPE 152 257  40  17
D253V4, multiclass
    clus
vv   SCML4 MUTATED SCML4 WILD-TYPE
  T1             3             152
  T2             4             257
  T3             3              40
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  SCML4 MUTATED     7   1     3
  SCML4 WILD-TYPE 300  88    69
D253V5, multiclass
       clus
vv      SCML4 MUTATED SCML4 WILD-TYPE
  N0                7             300
  N1                1              88
  N2+N3             3              69
[1] 3 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
  SCML4 MUTATED     6   0
  SCML4 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCML4 MUTATED      6    0
  SCML4 WILD-TYPE  321   23
   clus
vv  SCML4 MUTATED SCML4 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D253V7, binary
                 cls
clus                0   1
  SCML4 MUTATED     7   4
  SCML4 WILD-TYPE 252 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCML4 MUTATED      7    4
  SCML4 WILD-TYPE  252  217
        clus
vv       SCML4 MUTATED SCML4 WILD-TYPE
  FEMALE             7             252
  MALE               4             217
[1] 2 2
[1] FALSE
D253V8, continuous
[1] "Remove cluster labels:" "SCML4 MUTATED"         
clus
  SCML4 MUTATED SCML4 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8402      TCGA-62-A46O 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SCML4 MUTATED                            0                                 2
  SCML4 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SCML4 MUTATED                                                    6
  SCML4 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SCML4 MUTATED                                            0
  SCML4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SCML4 MUTATED                                               0
  SCML4 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SCML4 MUTATED                                0
  SCML4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SCML4 MUTATED                                    1
  SCML4 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SCML4 MUTATED                              0                             2
  SCML4 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SCML4 MUTATED                                               0
  SCML4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SCML4 MUTATED                              0
  SCML4 WILD-TYPE                            9
D253V9, multiclass
                                                    clus
vv                                                   SCML4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SCML4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V10, binary
                 cls
clus                0   1
  SCML4 MUTATED     1  10
  SCML4 WILD-TYPE  19 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCML4 MUTATED      1   10
  SCML4 WILD-TYPE   19  450
     clus
vv    SCML4 MUTATED SCML4 WILD-TYPE
  NO              1              19
  YES            10             450
[1] 2 2
[1] FALSE
D253V11, continuous
D253V12, continuous
[1] "Remove cluster labels:" "SCML4 MUTATED"         
clus
  SCML4 MUTATED SCML4 WILD-TYPE 
              2             255 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6642 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-6712      TCGA-55-6971      TCGA-55-7227      TCGA-55-7283 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7907 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-8089 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-8506      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8615      TCGA-55-8620      TCGA-55-8621 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-55-A491      TCGA-55-A492      TCGA-55-A493      TCGA-55-A494 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-62-8398      TCGA-64-1677      TCGA-64-1681      TCGA-64-5774 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-69-7761      TCGA-69-7763      TCGA-69-7764      TCGA-69-7765 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7979      TCGA-69-8253      TCGA-69-8255 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4675      TCGA-73-4676 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-73-7498      TCGA-75-6214      TCGA-75-7025      TCGA-75-7027 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7145      TCGA-78-7146      TCGA-78-7147 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-78-7148      TCGA-78-7149      TCGA-78-7150      TCGA-78-7152 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-78-7153      TCGA-78-7154      TCGA-78-7155      TCGA-78-7156 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-78-7158      TCGA-78-7159      TCGA-78-7160      TCGA-78-7161 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-78-7162      TCGA-78-7163      TCGA-78-7166      TCGA-78-7167 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-78-7220      TCGA-78-7535      TCGA-78-7536      TCGA-78-7537 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-78-7539      TCGA-78-7542      TCGA-78-7633      TCGA-78-8640 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-78-8648      TCGA-78-8655      TCGA-78-8660      TCGA-78-8662 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-80-5607      TCGA-80-5608      TCGA-83-5908      TCGA-86-6851 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7714      TCGA-86-7954      TCGA-86-8054 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8358      TCGA-86-8359      TCGA-86-8669 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-86-8673      TCGA-86-8674      TCGA-86-A456      TCGA-91-6829 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-91-6830      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7567      TCGA-95-7944      TCGA-95-7947 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8176 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-J2-8194      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4T2 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8      TCGA-MP-A4T9 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE      TCGA-MP-A4TF 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"SCML4 WILD-TYPE" "SCML4 WILD-TYPE" "SCML4 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  SCML4 MUTATED     4   0   1   1
  SCML4 WILD-TYPE 306  11   3  24
D253V13, multiclass
    clus
vv   SCML4 MUTATED SCML4 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             1               3
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCML4 MUTATED                                  0     0
  SCML4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCML4 MUTATED                           0     8
  SCML4 WILD-TYPE                        29   369
D253V14, multiclass
                                  clus
vv                                 SCML4 MUTATED SCML4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V15, binary
                 cls
clus                0   1
  SCML4 MUTATED     0   7
  SCML4 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCML4 MUTATED      0    7
  SCML4 WILD-TYPE    6  342
                        clus
vv                       SCML4 MUTATED SCML4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(254) Variable = SLC11A1 MUTATION ANALYSIS
D254V1, survival
                   sevent
clus2                 0   1
  SLC11A1 MUTATED     2   5
  SLC11A1 WILD-TYPE 313 136
  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
                7               449 
  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
                5               136 
$`SLC11A1 MUTATED`
TCGA-49-4488 TCGA-55-7728 TCGA-55-A4DF TCGA-78-7148 TCGA-78-7155 TCGA-91-6849 
       28.57         0.79        20.19        20.58        38.50         1.15 
TCGA-J2-A4AD 
       18.08 

$`SLC11A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
       23.51       163.10        27.16         5.69        19.27        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
       36.76         1.45         5.59        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
             0.79              0.00 
  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
            38.50            223.96 
  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
            20.19             17.92 
[1] "0.8 - 38.5 (20.2)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "3.3"
D254V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC11A1 MUTATED         0        3        2         0         1          1
  SLC11A1 WILD-TYPE       4      120      131        46        66         69
                   vv
clus                STAGE IIIB STAGE IV
  SLC11A1 MUTATED            0        0
  SLC11A1 WILD-TYPE         11       25
D254V3, multiclass
            clus
vv           SLC11A1 MUTATED SLC11A1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 3               120
  STAGE IB                 2               131
  STAGE IIA                0                46
  STAGE IIB                1                66
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC11A1 MUTATED     3   4   0   0
  SLC11A1 WILD-TYPE 152 257  43  18
D254V4, multiclass
    clus
vv   SLC11A1 MUTATED SLC11A1 WILD-TYPE
  T1               3               152
  T2               4               257
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  SLC11A1 MUTATED     5   1     1
  SLC11A1 WILD-TYPE 302  88    71
D254V5, multiclass
       clus
vv      SLC11A1 MUTATED SLC11A1 WILD-TYPE
  N0                  5               302
  N1                  1                88
  N2+N3               1                71
[1] 3 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
  SLC11A1 MUTATED     2   0
  SLC11A1 WILD-TYPE 325  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A1 MUTATED      2    0
  SLC11A1 WILD-TYPE  325   23
   clus
vv  SLC11A1 MUTATED SLC11A1 WILD-TYPE
  0               2               325
  1               0                23
[1] 2 2
[1] FALSE
D254V7, binary
                   cls
clus                  0   1
  SLC11A1 MUTATED     4   3
  SLC11A1 WILD-TYPE 255 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A1 MUTATED      4    3
  SLC11A1 WILD-TYPE  255  218
        clus
vv       SLC11A1 MUTATED SLC11A1 WILD-TYPE
  FEMALE               4               255
  MALE                 3               218
[1] 2 2
[1] FALSE
D254V8, continuous
[1] "Remove cluster labels:" "SLC11A1 MUTATED"       
clus
  SLC11A1 MUTATED SLC11A1 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A4JF        TCGA-86-A4P7        TCGA-93-7348 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" "SLC11A1 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC11A1 MUTATED                            0
  SLC11A1 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC11A1 MUTATED                                   1
  SLC11A1 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC11A1 MUTATED                                                    5
  SLC11A1 WILD-TYPE                                                289
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC11A1 MUTATED                                            0
  SLC11A1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC11A1 MUTATED                                               0
  SLC11A1 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC11A1 MUTATED                                0
  SLC11A1 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC11A1 MUTATED                                    0
  SLC11A1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC11A1 MUTATED                              0                             0
  SLC11A1 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC11A1 MUTATED                                               0
  SLC11A1 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC11A1 MUTATED                              1
  SLC11A1 WILD-TYPE                            8
D254V9, multiclass
                                                    clus
vv                                                   SLC11A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   SLC11A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V10, binary
                   cls
clus                  0   1
  SLC11A1 MUTATED     0   7
  SLC11A1 WILD-TYPE  20 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A1 MUTATED      0    7
  SLC11A1 WILD-TYPE   20  453
     clus
vv    SLC11A1 MUTATED SLC11A1 WILD-TYPE
  NO                0                20
  YES               7               453
[1] 2 2
[1] FALSE
D254V11, continuous
D254V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC11A1 MUTATED     5   0   0   1
  SLC11A1 WILD-TYPE 305  11   4  24
D254V13, multiclass
    clus
vv   SLC11A1 MUTATED SLC11A1 WILD-TYPE
  R0               5               305
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC11A1 MUTATED                                  0     0
  SLC11A1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC11A1 MUTATED                           1     5
  SLC11A1 WILD-TYPE                        28   372
D254V14, multiclass
                                  clus
vv                                 SLC11A1 MUTATED SLC11A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          5               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V15, binary
                   cls
clus                  0   1
  SLC11A1 MUTATED     0   4
  SLC11A1 WILD-TYPE   6 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A1 MUTATED      0    4
  SLC11A1 WILD-TYPE    6  345
                        clus
vv                       SLC11A1 MUTATED SLC11A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               4               345
[1] 2 2
[1] FALSE

Clustering(255) Variable = MOGAT3 MUTATION ANALYSIS
D255V1, survival
                  sevent
clus2                0   1
  MOGAT3 MUTATED     7   2
  MOGAT3 WILD-TYPE 308 139
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
               9              447 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
               2              139 
$`MOGAT3 MUTATED`
TCGA-05-4398 TCGA-55-6981 TCGA-55-7994 TCGA-55-8507 TCGA-55-8619 TCGA-69-7978 
       47.05        45.34        19.82         0.26         1.61         2.30 
TCGA-78-7535 TCGA-99-8028 TCGA-MN-A4N4 
       31.20        36.76        38.63 

$`MOGAT3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 
       48.49         3.88         5.49         7.79         2.20        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.36         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 
       20.84        18.67        20.68        24.56        34.85         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
            0.26             0.00 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
           47.05           223.96 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
           31.20            17.92 
[1] "0.3 - 47.0 (31.2)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.6"
D255V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MOGAT3 MUTATED         0        3        2         0         3          1
  MOGAT3 WILD-TYPE       4      120      131        46        64         69
                  vv
clus               STAGE IIIB STAGE IV
  MOGAT3 MUTATED            1        0
  MOGAT3 WILD-TYPE         10       25
D255V3, multiclass
            clus
vv           MOGAT3 MUTATED MOGAT3 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                2              131
  STAGE IIA               0               46
  STAGE IIB               3               64
  STAGE IIIA              1               69
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MOGAT3 MUTATED     4   3   2   1
  MOGAT3 WILD-TYPE 151 258  41  17
D255V4, multiclass
    clus
vv   MOGAT3 MUTATED MOGAT3 WILD-TYPE
  T1              4              151
  T2              3              258
  T3              2               41
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  MOGAT3 MUTATED     7   1     2
  MOGAT3 WILD-TYPE 300  88    70
D255V5, multiclass
       clus
vv      MOGAT3 MUTATED MOGAT3 WILD-TYPE
  N0                 7              300
  N1                 1               88
  N2+N3              2               70
[1] 3 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
  MOGAT3 MUTATED     6   0
  MOGAT3 WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      6    0
  MOGAT3 WILD-TYPE  321   23
   clus
vv  MOGAT3 MUTATED MOGAT3 WILD-TYPE
  0              6              321
  1              0               23
[1] 2 2
[1] FALSE
D255V7, binary
                  cls
clus                 0   1
  MOGAT3 MUTATED     4   6
  MOGAT3 WILD-TYPE 255 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      4    6
  MOGAT3 WILD-TYPE  255  215
        clus
vv       MOGAT3 MUTATED MOGAT3 WILD-TYPE
  FEMALE              4              255
  MALE                6              215
[1] 2 2
[1] FALSE
D255V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MOGAT3 MUTATED                            0                                 2
  MOGAT3 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MOGAT3 MUTATED                                                    7
  MOGAT3 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MOGAT3 MUTATED                                            0
  MOGAT3 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MOGAT3 MUTATED                                               0
  MOGAT3 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  MOGAT3 MUTATED                                0
  MOGAT3 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  MOGAT3 MUTATED                                    0
  MOGAT3 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MOGAT3 MUTATED                              0                             0
  MOGAT3 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MOGAT3 MUTATED                                               0
  MOGAT3 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  MOGAT3 MUTATED                              1
  MOGAT3 WILD-TYPE                            8
D255V9, multiclass
                                                    clus
vv                                                   MOGAT3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    1
                                                    clus
vv                                                   MOGAT3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V10, binary
                  cls
clus                 0   1
  MOGAT3 MUTATED     0  10
  MOGAT3 WILD-TYPE  20 450
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      0   10
  MOGAT3 WILD-TYPE   20  450
     clus
vv    MOGAT3 MUTATED MOGAT3 WILD-TYPE
  NO               0               20
  YES             10              450
[1] 2 2
[1] FALSE
D255V11, continuous
D255V12, continuous
                  vv
clus                R0  R1  R2  RX
  MOGAT3 MUTATED     9   0   0   0
  MOGAT3 WILD-TYPE 301  11   4  25
D255V13, multiclass
    clus
vv   MOGAT3 MUTATED MOGAT3 WILD-TYPE
  R0              9              301
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOGAT3 MUTATED                                  0     0
  MOGAT3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MOGAT3 MUTATED                           1     7
  MOGAT3 WILD-TYPE                        28   370
D255V14, multiclass
                                  clus
vv                                 MOGAT3 MUTATED MOGAT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V15, binary
                  cls
clus                 0   1
  MOGAT3 MUTATED     0   7
  MOGAT3 WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      0    7
  MOGAT3 WILD-TYPE    6  342
                        clus
vv                       MOGAT3 MUTATED MOGAT3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(256) Variable = TULP4 MUTATION ANALYSIS
D256V1, survival
                 sevent
clus2               0   1
  TULP4 MUTATED    11   1
  TULP4 WILD-TYPE 304 140
  TULP4 MUTATED TULP4 WILD-TYPE 
             12             444 
  TULP4 MUTATED TULP4 WILD-TYPE 
              1             140 
$`TULP4 MUTATED`
TCGA-44-7667 TCGA-49-6744 TCGA-50-5941 TCGA-55-6987 TCGA-55-8089 TCGA-62-8394 
       36.07        29.26        18.64        70.26         3.29         4.57 
TCGA-69-7980 TCGA-73-4670 TCGA-78-7159 TCGA-78-7539 TCGA-78-8655 TCGA-97-A4M7 
       12.56         4.31        64.90        10.75        77.59        20.68 

$`TULP4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       29.46        29.75        55.89        14.63        12.13        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       40.60        78.67        21.47         8.45        15.12        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30         2.93        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       29.98        26.30        15.35         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       20.52        17.75        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  TULP4 MUTATED TULP4 WILD-TYPE 
           3.29            0.00 
  TULP4 MUTATED TULP4 WILD-TYPE 
          77.59          223.96 
  TULP4 MUTATED TULP4 WILD-TYPE 
          19.66           17.95 
[1] "3.3 - 77.6 (19.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "5.1"
D256V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TULP4 MUTATED         1        6        0         2         1          1
  TULP4 WILD-TYPE       3      117      133        44        66         69
                 vv
clus              STAGE IIIB STAGE IV
  TULP4 MUTATED            1        1
  TULP4 WILD-TYPE         10       24
D256V3, multiclass
            clus
vv           TULP4 MUTATED TULP4 WILD-TYPE
  STAGE I                1               3
  STAGE IA               6             117
  STAGE IB               0             133
  STAGE IIA              2              44
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TULP4 MUTATED     7   4   1   1
  TULP4 WILD-TYPE 148 257  42  17
D256V4, multiclass
    clus
vv   TULP4 MUTATED TULP4 WILD-TYPE
  T1             7             148
  T2             4             257
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  TULP4 MUTATED     9   1     2
  TULP4 WILD-TYPE 298  88    70
D256V5, multiclass
       clus
vv      TULP4 MUTATED TULP4 WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             2              70
[1] 3 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
  TULP4 MUTATED    10   1
  TULP4 WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP4 MUTATED     10    1
  TULP4 WILD-TYPE  317   22
   clus
vv  TULP4 MUTATED TULP4 WILD-TYPE
  0            10             317
  1             1              22
[1] 2 2
[1] FALSE
D256V7, binary
                 cls
clus                0   1
  TULP4 MUTATED    10   3
  TULP4 WILD-TYPE 249 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP4 MUTATED     10    3
  TULP4 WILD-TYPE  249  218
        clus
vv       TULP4 MUTATED TULP4 WILD-TYPE
  FEMALE            10             249
  MALE               3             218
[1] 2 2
[1] FALSE
D256V8, continuous
[1] "Remove cluster labels:" "TULP4 MUTATED"         
clus
  TULP4 MUTATED TULP4 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"TULP4 WILD-TYPE" "TULP4 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TULP4 MUTATED                            0                                 6
  TULP4 WILD-TYPE                         18                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TULP4 MUTATED                                                    7
  TULP4 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TULP4 MUTATED                                            0
  TULP4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TULP4 MUTATED                                               0
  TULP4 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TULP4 MUTATED                                0
  TULP4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TULP4 MUTATED                                    0
  TULP4 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TULP4 MUTATED                              0                             0
  TULP4 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TULP4 MUTATED                                               0
  TULP4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TULP4 MUTATED                              0
  TULP4 WILD-TYPE                            9
D256V9, multiclass
                                                    clus
vv                                                   TULP4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   TULP4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V10, binary
                 cls
clus                0   1
  TULP4 MUTATED     0  13
  TULP4 WILD-TYPE  20 447
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP4 MUTATED      0   13
  TULP4 WILD-TYPE   20  447
     clus
vv    TULP4 MUTATED TULP4 WILD-TYPE
  NO              0              20
  YES            13             447
[1] 2 2
[1] FALSE
D256V11, continuous
D256V12, continuous
                 vv
clus               R0  R1  R2  RX
  TULP4 MUTATED     9   0   0   0
  TULP4 WILD-TYPE 301  11   4  25
D256V13, multiclass
    clus
vv   TULP4 MUTATED TULP4 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TULP4 MUTATED                                  0     0
  TULP4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TULP4 MUTATED                           0    11
  TULP4 WILD-TYPE                        29   366
D256V14, multiclass
                                  clus
vv                                 TULP4 MUTATED TULP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V15, binary
                 cls
clus                0   1
  TULP4 MUTATED     0   7
  TULP4 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP4 MUTATED      0    7
  TULP4 WILD-TYPE    6  342
                        clus
vv                       TULP4 MUTATED TULP4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(257) Variable = ASB5 MUTATION ANALYSIS
D257V1, survival
                sevent
clus2              0   1
  ASB5 MUTATED     9   4
  ASB5 WILD-TYPE 306 137
  ASB5 MUTATED ASB5 WILD-TYPE 
            13            443 
  ASB5 MUTATED ASB5 WILD-TYPE 
             4            137 
$`ASB5 MUTATED`
TCGA-05-4382 TCGA-38-4632 TCGA-44-6774 TCGA-44-7669 TCGA-50-6592 TCGA-55-7725 
       19.96        44.61        21.63        18.87        25.55         1.28 
TCGA-55-A4DG TCGA-69-7980 TCGA-78-7537 TCGA-78-7539 TCGA-86-8585 TCGA-95-7039 
       19.99        12.56        53.33        10.75         1.15         1.12 
TCGA-99-8032 
        1.45 

$`ASB5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 
       14.60        19.46        12.03         7.17        36.07        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55        42.35         3.91        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        15.81        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30         2.93        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        8.02        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ASB5 MUTATED ASB5 WILD-TYPE 
          1.12           0.00 
  ASB5 MUTATED ASB5 WILD-TYPE 
         53.33         223.96 
  ASB5 MUTATED ASB5 WILD-TYPE 
         18.87          17.98 
[1] "1.1 - 53.3 (18.9)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.3"
D257V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ASB5 MUTATED         1        3        4         2         1          2
  ASB5 WILD-TYPE       3      120      129        44        66         68
                vv
clus             STAGE IIIB STAGE IV
  ASB5 MUTATED            0        1
  ASB5 WILD-TYPE         11       24
D257V3, multiclass
            clus
vv           ASB5 MUTATED ASB5 WILD-TYPE
  STAGE I               1              3
  STAGE IA              3            120
  STAGE IB              4            129
  STAGE IIA             2             44
  STAGE IIB             1             66
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ASB5 MUTATED     6   7   1   0
  ASB5 WILD-TYPE 149 254  42  18
D257V4, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  T1            6            149
  T2            7            254
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  ASB5 MUTATED    10   2     2
  ASB5 WILD-TYPE 297  87    70
D257V5, multiclass
       clus
vv      ASB5 MUTATED ASB5 WILD-TYPE
  N0              10            297
  N1               2             87
  N2+N3            2             70
[1] 3 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
  ASB5 MUTATED     9   1
  ASB5 WILD-TYPE 318  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      9    1
  ASB5 WILD-TYPE  318   22
   clus
vv  ASB5 MUTATED ASB5 WILD-TYPE
  0            9            318
  1            1             22
[1] 2 2
[1] FALSE
D257V7, binary
                cls
clus               0   1
  ASB5 MUTATED     7   7
  ASB5 WILD-TYPE 252 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      7    7
  ASB5 WILD-TYPE  252  214
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  FEMALE            7            252
  MALE              7            214
[1] 2 2
[1] FALSE
D257V8, continuous
[1] "Remove cluster labels:" "ASB5 MUTATED"          
clus
  ASB5 MUTATED ASB5 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7910     TCGA-55-7914 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8205     TCGA-55-8208 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ASB5 MUTATED                            0                                 4
  ASB5 WILD-TYPE                         18                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASB5 MUTATED                                                    9
  ASB5 WILD-TYPE                                                285
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ASB5 MUTATED                                            0
  ASB5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ASB5 MUTATED                                               0
  ASB5 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  ASB5 MUTATED                                0
  ASB5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  ASB5 MUTATED                                    0
  ASB5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ASB5 MUTATED                              0                             0
  ASB5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ASB5 MUTATED                                               1
  ASB5 WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  ASB5 MUTATED                              0
  ASB5 WILD-TYPE                            9
D257V9, multiclass
                                                    clus
vv                                                   ASB5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   ASB5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V10, binary
                cls
clus               0   1
  ASB5 MUTATED     1  13
  ASB5 WILD-TYPE  19 447
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      1   13
  ASB5 WILD-TYPE   19  447
     clus
vv    ASB5 MUTATED ASB5 WILD-TYPE
  NO             1             19
  YES           13            447
[1] 2 2
[1] FALSE
D257V11, continuous
D257V12, continuous
                vv
clus              R0  R1  R2  RX
  ASB5 MUTATED     9   0   0   0
  ASB5 WILD-TYPE 301  11   4  25
D257V13, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  R0            9            301
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASB5 MUTATED                                  0     0
  ASB5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ASB5 MUTATED                           2     9
  ASB5 WILD-TYPE                        27   368
D257V14, multiclass
                                  clus
vv                                 ASB5 MUTATED ASB5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                       9            368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V15, binary
                cls
clus               0   1
  ASB5 MUTATED     0  10
  ASB5 WILD-TYPE   6 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      0   10
  ASB5 WILD-TYPE    6  339
                        clus
vv                       ASB5 MUTATED ASB5 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(258) Variable = TDRD6 MUTATION ANALYSIS
D258V1, survival
                 sevent
clus2               0   1
  TDRD6 MUTATED    16   1
  TDRD6 WILD-TYPE 299 140
  TDRD6 MUTATED TDRD6 WILD-TYPE 
             17             439 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
              1             140 
$`TDRD6 MUTATED`
TCGA-05-4430 TCGA-35-4122 TCGA-44-7660 TCGA-55-7727 TCGA-55-7815 TCGA-55-8207 
       25.02         7.40        19.46         1.12         1.78         2.17 
TCGA-55-8208 TCGA-55-8507 TCGA-69-7979 TCGA-86-8073 TCGA-86-A4JF TCGA-91-A4BC 
       22.16         0.26         2.93        24.33        17.62         1.45 
TCGA-97-7553 TCGA-97-7938 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4TH 
       43.79         0.59        38.63         2.76        14.66 

$`TDRD6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        14.60        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 
       23.18         1.28         1.28         0.79         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.18        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       25.48         5.95         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4SV 
       19.00        14.30         3.81         0.20        27.19        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  TDRD6 MUTATED TDRD6 WILD-TYPE 
           0.26            0.00 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
          43.79          223.96 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
           7.40           18.18 
[1] "0.3 - 43.8 (7.4)"   "0.0 - 224.0 (18.2)"
[1] "hr=" "2.8"
D258V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TDRD6 MUTATED         0        8        6         1         1          1
  TDRD6 WILD-TYPE       4      115      127        45        66         69
                 vv
clus              STAGE IIIB STAGE IV
  TDRD6 MUTATED            0        0
  TDRD6 WILD-TYPE         11       25
D258V3, multiclass
            clus
vv           TDRD6 MUTATED TDRD6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               8             115
  STAGE IB               6             127
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TDRD6 MUTATED     9   7   1   0
  TDRD6 WILD-TYPE 146 254  42  18
D258V4, multiclass
    clus
vv   TDRD6 MUTATED TDRD6 WILD-TYPE
  T1             9             146
  T2             7             254
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  TDRD6 MUTATED    16   0     1
  TDRD6 WILD-TYPE 291  89    71
D258V5, multiclass
       clus
vv      TDRD6 MUTATED TDRD6 WILD-TYPE
  N0               16             291
  N1                0              89
  N2+N3             1              71
[1] 3 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
  TDRD6 MUTATED     8   0
  TDRD6 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      8    0
  TDRD6 WILD-TYPE  319   23
   clus
vv  TDRD6 MUTATED TDRD6 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D258V7, binary
                 cls
clus                0   1
  TDRD6 MUTATED     6  11
  TDRD6 WILD-TYPE 253 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      6   11
  TDRD6 WILD-TYPE  253  210
        clus
vv       TDRD6 MUTATED TDRD6 WILD-TYPE
  FEMALE             6             253
  MALE              11             210
[1] 2 2
[1] FALSE
D258V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TDRD6 MUTATED                            2                                 1
  TDRD6 WILD-TYPE                         16                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TDRD6 MUTATED                                                   11
  TDRD6 WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TDRD6 MUTATED                                            0
  TDRD6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TDRD6 MUTATED                                               3
  TDRD6 WILD-TYPE                                            16
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TDRD6 MUTATED                                0
  TDRD6 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TDRD6 MUTATED                                    0
  TDRD6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TDRD6 MUTATED                              0                             0
  TDRD6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TDRD6 MUTATED                                               0
  TDRD6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TDRD6 MUTATED                              0
  TDRD6 WILD-TYPE                            9
D258V9, multiclass
                                                    clus
vv                                                   TDRD6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   TDRD6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V10, binary
                 cls
clus                0   1
  TDRD6 MUTATED     0  17
  TDRD6 WILD-TYPE  20 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      0   17
  TDRD6 WILD-TYPE   20  443
     clus
vv    TDRD6 MUTATED TDRD6 WILD-TYPE
  NO              0              20
  YES            17             443
[1] 2 2
[1] FALSE
D258V11, continuous
D258V12, continuous
                 vv
clus               R0  R1  R2  RX
  TDRD6 MUTATED    13   0   0   0
  TDRD6 WILD-TYPE 297  11   4  25
D258V13, multiclass
    clus
vv   TDRD6 MUTATED TDRD6 WILD-TYPE
  R0            13             297
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TDRD6 MUTATED                                  0     0
  TDRD6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TDRD6 MUTATED                           0    15
  TDRD6 WILD-TYPE                        29   362
D258V14, multiclass
                                  clus
vv                                 TDRD6 MUTATED TDRD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       15             362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V15, binary
                 cls
clus                0   1
  TDRD6 MUTATED     0  15
  TDRD6 WILD-TYPE   6 334
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      0   15
  TDRD6 WILD-TYPE    6  334
                        clus
vv                       TDRD6 MUTATED TDRD6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            15             334
[1] 2 2
[1] FALSE

Clustering(259) Variable = COL12A1 MUTATION ANALYSIS
D259V1, survival
                   sevent
clus2                 0   1
  COL12A1 MUTATED    35  16
  COL12A1 WILD-TYPE 280 125
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               51               405 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               16               125 
$`COL12A1 MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4405 TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 
       50.07        19.96        20.05        22.03         8.68        97.74 
TCGA-44-6144 TCGA-44-7667 TCGA-44-7670 TCGA-44-A479 TCGA-49-6767 TCGA-50-5072 
       23.77        36.07        29.00        15.98        22.26         8.22 
TCGA-50-5930 TCGA-50-5933 TCGA-50-7109 TCGA-53-7624 TCGA-55-6968 TCGA-55-7994 
        9.27        78.67        10.13        34.29        42.51        19.82 
TCGA-55-8085 TCGA-55-8207 TCGA-55-A4DF TCGA-62-A46O TCGA-62-A46V TCGA-64-1676 
       29.72         2.17        20.19        47.80        72.30        56.81 
TCGA-64-5779 TCGA-67-3773 TCGA-73-4670 TCGA-78-7155 TCGA-78-7220 TCGA-78-7539 
       28.41        14.04         4.31        38.50        26.53        10.75 
TCGA-78-7542 TCGA-86-7701 TCGA-86-7711 TCGA-86-7954 TCGA-86-8073 TCGA-86-8074 
       10.55        31.13        34.39        19.89        24.33         0.79 
TCGA-86-8279 TCGA-91-6848 TCGA-95-7039 TCGA-95-7043 TCGA-97-7546 TCGA-97-8174 
       15.85         7.36         1.12         1.22        31.69         5.39 
TCGA-99-7458 TCGA-99-8025 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SY TCGA-MP-A4TA 
       24.56        34.85         0.20        38.63        49.35        31.23 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-NJ-A55R 
       14.66        19.13        19.82 

$`COL12A1 WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
        3.98        14.01        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
       24.03        47.05         8.02        19.00         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
        4.96        29.00         9.04         2.04         7.40         5.98 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        28.37        12.59        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       14.63        12.13        29.26        17.16        11.64        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 
       11.05        12.16         6.21        41.69         0.72        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       48.62         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8087 
        0.53         6.48        17.65         6.15         0.16        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.08         1.51        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        19.53        56.71        54.35        67.96 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 
       13.61        39.25        40.96        29.92        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98         2.04        42.90        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       20.05        18.84         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30        15.35         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
        8.48        88.14        31.20         8.02        53.33        39.35 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       27.09        12.36         5.88        13.87        20.55        19.43 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 
       16.70        24.49         4.08         4.57        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.65        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       17.29         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       27.29         2.76        21.40        18.18        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        20.68        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
       19.00        14.30         3.81        27.19         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       58.45        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
       41.59         2.43        10.09        29.46        11.05        14.10 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.26         0.43        59.11 

  COL12A1 MUTATED COL12A1 WILD-TYPE 
              0.2               0.0 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
            97.74            223.96 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
            22.03             17.59 
[1] "0.2 - 97.7 (22.0)"  "0.0 - 224.0 (17.6)"
[1] "hr=" "1.1"
D259V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL12A1 MUTATED         0       12       16         7         6          8
  COL12A1 WILD-TYPE       4      111      117        39        61         62
                   vv
clus                STAGE IIIB STAGE IV
  COL12A1 MUTATED            1        4
  COL12A1 WILD-TYPE         10       21
D259V3, multiclass
            clus
vv           COL12A1 MUTATED COL12A1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                12               111
  STAGE IB                16               117
  STAGE IIA                7                39
  STAGE IIB                6                61
  STAGE IIIA               8                62
  STAGE IIIB               1                10
  STAGE IV                 4                21
[1] 8 2
[1] TRUE
[1] "dimension of 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    16  31   5   2
  COL12A1 WILD-TYPE 139 230  38  16
D259V4, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  T1              16               139
  T2              31               230
  T3               5                38
  T4               2                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"
                   vv
clus                 N0  N1 N2+N3
  COL12A1 MUTATED    39   7     8
  COL12A1 WILD-TYPE 268  82    64
D259V5, multiclass
       clus
vv      COL12A1 MUTATED COL12A1 WILD-TYPE
  N0                 39               268
  N1                  7                82
  N2+N3               8                64
[1] 3 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
  COL12A1 MUTATED    37   4
  COL12A1 WILD-TYPE 290  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     37    4
  COL12A1 WILD-TYPE  290   19
   clus
vv  COL12A1 MUTATED COL12A1 WILD-TYPE
  0              37               290
  1               4                19
[1] 2 2
[1] FALSE
D259V7, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    24  30
  COL12A1 WILD-TYPE 235 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     24   30
  COL12A1 WILD-TYPE  235  191
        clus
vv       COL12A1 MUTATED COL12A1 WILD-TYPE
  FEMALE              24               235
  MALE                30               191
[1] 2 2
[1] FALSE
D259V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  COL12A1 MUTATED                            3
  COL12A1 WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL12A1 MUTATED                                  10
  COL12A1 WILD-TYPE                                92
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL12A1 MUTATED                                                   35
  COL12A1 WILD-TYPE                                                259
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL12A1 MUTATED                                            0
  COL12A1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL12A1 MUTATED                                               3
  COL12A1 WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  COL12A1 MUTATED                                0
  COL12A1 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  COL12A1 MUTATED                                    0
  COL12A1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL12A1 MUTATED                              0                             2
  COL12A1 WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL12A1 MUTATED                                               1
  COL12A1 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  COL12A1 MUTATED                              0
  COL12A1 WILD-TYPE                            9
D259V9, multiclass
                                                    clus
vv                                                   COL12A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              35
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   COL12A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               259
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V10, binary
                   cls
clus                  0   1
  COL12A1 MUTATED     5  49
  COL12A1 WILD-TYPE  15 411
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED      5   49
  COL12A1 WILD-TYPE   15  411
     clus
vv    COL12A1 MUTATED COL12A1 WILD-TYPE
  NO                5                15
  YES              49               411
[1] 2 2
[1] FALSE
D259V11, continuous
D259V12, continuous
                   vv
clus                 R0  R1  R2  RX
  COL12A1 MUTATED    40   0   0   2
  COL12A1 WILD-TYPE 270  11   4  23
D259V13, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  R0              40               270
  R1               0                11
  R2               0                 4
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL12A1 MUTATED                                  0     0
  COL12A1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COL12A1 MUTATED                           2    44
  COL12A1 WILD-TYPE                        27   333
D259V14, multiclass
                                  clus
vv                                 COL12A1 MUTATED COL12A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         44               333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V15, binary
                   cls
clus                  0   1
  COL12A1 MUTATED     3  38
  COL12A1 WILD-TYPE   3 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED      3   38
  COL12A1 WILD-TYPE    3  311
                        clus
vv                       COL12A1 MUTATED COL12A1 WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              38               311
[1] 2 2
[1] FALSE

Clustering(260) Variable = SMOC1 MUTATION ANALYSIS
D260V1, survival
                 sevent
clus2               0   1
  SMOC1 MUTATED     7   5
  SMOC1 WILD-TYPE 308 136
  SMOC1 MUTATED SMOC1 WILD-TYPE 
             12             444 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
              5             136 
$`SMOC1 MUTATED`
TCGA-44-2656 TCGA-44-8117 TCGA-49-6745 TCGA-50-6590 TCGA-55-7911 TCGA-55-8299 
       46.98        12.66        17.16        42.35        17.65        15.42 
TCGA-62-A46O TCGA-69-7979 TCGA-78-7537 TCGA-99-7458 TCGA-99-8025 TCGA-MP-A4TK 
       47.80         2.93        53.33        24.56        34.85        19.13 

$`SMOC1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
       36.07        18.87        29.00        17.59        23.64         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 
       29.75        55.89        14.63        12.13        29.26        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        22.55         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         0.53         6.48         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       20.68        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SMOC1 MUTATED SMOC1 WILD-TYPE 
           2.93            0.00 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
          53.33          223.96 
  SMOC1 MUTATED SMOC1 WILD-TYPE 
         21.845          17.950 
[1] "2.9 - 53.3 (21.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D260V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SMOC1 MUTATED         0        2        6         0         1          3
  SMOC1 WILD-TYPE       4      121      127        46        66         67
                 vv
clus              STAGE IIIB STAGE IV
  SMOC1 MUTATED            0        0
  SMOC1 WILD-TYPE         11       25
D260V3, multiclass
            clus
vv           SMOC1 MUTATED SMOC1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               6             127
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMOC1 MUTATED     2   8   1   1
  SMOC1 WILD-TYPE 153 253  42  17
D260V4, multiclass
    clus
vv   SMOC1 MUTATED SMOC1 WILD-TYPE
  T1             2             153
  T2             8             253
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  SMOC1 MUTATED     9   1     2
  SMOC1 WILD-TYPE 298  88    70
D260V5, multiclass
       clus
vv      SMOC1 MUTATED SMOC1 WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             2              70
[1] 3 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
  SMOC1 MUTATED     8   0
  SMOC1 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMOC1 MUTATED      8    0
  SMOC1 WILD-TYPE  319   23
   clus
vv  SMOC1 MUTATED SMOC1 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D260V7, binary
                 cls
clus                0   1
  SMOC1 MUTATED     9   3
  SMOC1 WILD-TYPE 250 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMOC1 MUTATED      9    3
  SMOC1 WILD-TYPE  250  218
        clus
vv       SMOC1 MUTATED SMOC1 WILD-TYPE
  FEMALE             9             250
  MALE               3             218
[1] 2 2
[1] FALSE
D260V8, continuous
[1] "Remove cluster labels:" "SMOC1 MUTATED"         
clus
  SMOC1 MUTATED SMOC1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-MN-A4N1 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"SMOC1 WILD-TYPE" "SMOC1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SMOC1 MUTATED                            1                                 1
  SMOC1 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SMOC1 MUTATED                                                    9
  SMOC1 WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SMOC1 MUTATED                                            0
  SMOC1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SMOC1 MUTATED                                               1
  SMOC1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SMOC1 MUTATED                                0
  SMOC1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SMOC1 MUTATED                                    0
  SMOC1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SMOC1 MUTATED                              0                             0
  SMOC1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SMOC1 MUTATED                                               0
  SMOC1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SMOC1 MUTATED                              0
  SMOC1 WILD-TYPE                            9
D260V9, multiclass
                                                    clus
vv                                                   SMOC1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SMOC1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V10, binary
                 cls
clus                0   1
  SMOC1 MUTATED     0  12
  SMOC1 WILD-TYPE  20 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMOC1 MUTATED      0   12
  SMOC1 WILD-TYPE   20  448
     clus
vv    SMOC1 MUTATED SMOC1 WILD-TYPE
  NO              0              20
  YES            12             448
[1] 2 2
[1] FALSE
D260V11, continuous
D260V12, continuous
                 vv
clus               R0  R1  R2  RX
  SMOC1 MUTATED     7   0   0   0
  SMOC1 WILD-TYPE 303  11   4  25
D260V13, multiclass
    clus
vv   SMOC1 MUTATED SMOC1 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMOC1 MUTATED                                  0     0
  SMOC1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMOC1 MUTATED                           1     9
  SMOC1 WILD-TYPE                        28   368
D260V14, multiclass
                                  clus
vv                                 SMOC1 MUTATED SMOC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V15, binary
                 cls
clus                0   1
  SMOC1 MUTATED     0   9
  SMOC1 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMOC1 MUTATED      0    9
  SMOC1 WILD-TYPE    6  340
                        clus
vv                       SMOC1 MUTATED SMOC1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(261) Variable = HSD11B1 MUTATION ANALYSIS
D261V1, survival
                   sevent
clus2                 0   1
  HSD11B1 MUTATED     6   1
  HSD11B1 WILD-TYPE 309 140
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                7               449 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                1               140 
$`HSD11B1 MUTATED`
TCGA-44-3918 TCGA-44-8117 TCGA-44-A47A TCGA-55-A491 TCGA-67-3773 TCGA-78-7155 
       34.06        12.66        15.32        20.58        14.04        38.50 
TCGA-78-8640 
      214.62 

$`HSD11B1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        38.24         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
       36.07        18.87        29.00        17.59        23.64         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40         1.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 
       28.41        51.25        28.47        20.05        18.84         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       10.55        32.68        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
            12.66              0.00 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           214.62            223.96 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
            20.58             17.98 
[1] "12.7 - 214.6 (20.6)" "0.0 - 224.0 (18.0)" 
[1] "hr=" "4.1"
D261V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HSD11B1 MUTATED         0        2        4         1         0          0
  HSD11B1 WILD-TYPE       4      121      129        45        67         70
                   vv
clus                STAGE IIIB STAGE IV
  HSD11B1 MUTATED            0        0
  HSD11B1 WILD-TYPE         11       25
D261V3, multiclass
            clus
vv           HSD11B1 MUTATED HSD11B1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 4               129
  STAGE IIA                1                45
  STAGE IIB                0                67
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HSD11B1 MUTATED     3   4   0   0
  HSD11B1 WILD-TYPE 152 257  43  18
D261V4, multiclass
    clus
vv   HSD11B1 MUTATED HSD11B1 WILD-TYPE
  T1               3               152
  T2               4               257
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  HSD11B1 MUTATED     6   1     0
  HSD11B1 WILD-TYPE 301  88    72
D261V5, multiclass
       clus
vv      HSD11B1 MUTATED HSD11B1 WILD-TYPE
  N0                  6               301
  N1                  1                88
  N2+N3               0                72
[1] 3 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
  HSD11B1 MUTATED     5   0
  HSD11B1 WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      5    0
  HSD11B1 WILD-TYPE  322   23
   clus
vv  HSD11B1 MUTATED HSD11B1 WILD-TYPE
  0               5               322
  1               0                23
[1] 2 2
[1] FALSE
D261V7, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     5   2
  HSD11B1 WILD-TYPE 254 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      5    2
  HSD11B1 WILD-TYPE  254  219
        clus
vv       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  FEMALE               5               254
  MALE                 2               219
[1] 2 2
[1] FALSE
D261V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  HSD11B1 MUTATED                            0
  HSD11B1 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  HSD11B1 MUTATED                                   0
  HSD11B1 WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HSD11B1 MUTATED                                                    7
  HSD11B1 WILD-TYPE                                                287
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HSD11B1 MUTATED                                            0
  HSD11B1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HSD11B1 MUTATED                                               0
  HSD11B1 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  HSD11B1 MUTATED                                0
  HSD11B1 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  HSD11B1 MUTATED                                    0
  HSD11B1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HSD11B1 MUTATED                              0                             0
  HSD11B1 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HSD11B1 MUTATED                                               0
  HSD11B1 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  HSD11B1 MUTATED                              0
  HSD11B1 WILD-TYPE                            9
D261V9, multiclass
                                                    clus
vv                                                   HSD11B1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   HSD11B1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V10, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     0   7
  HSD11B1 WILD-TYPE  20 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      0    7
  HSD11B1 WILD-TYPE   20  453
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO                0                20
  YES               7               453
[1] 2 2
[1] FALSE
D261V11, continuous
D261V12, continuous
                   vv
clus                 R0  R1  R2  RX
  HSD11B1 MUTATED     6   0   0   0
  HSD11B1 WILD-TYPE 304  11   4  25
D261V13, multiclass
    clus
vv   HSD11B1 MUTATED HSD11B1 WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSD11B1 MUTATED                                  0     0
  HSD11B1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HSD11B1 MUTATED                           0     6
  HSD11B1 WILD-TYPE                        29   371
D261V14, multiclass
                                  clus
vv                                 HSD11B1 MUTATED HSD11B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V15, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     0   5
  HSD11B1 WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      0    5
  HSD11B1 WILD-TYPE    6  344
                        clus
vv                       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(262) Variable = COL7A1 MUTATION ANALYSIS
D262V1, survival
                  sevent
clus2                0   1
  COL7A1 MUTATED    25   6
  COL7A1 WILD-TYPE 290 135
  COL7A1 MUTATED COL7A1 WILD-TYPE 
              31              425 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
               6              135 
$`COL7A1 MUTATED`
TCGA-05-4398 TCGA-05-4415 TCGA-05-5425 TCGA-44-6777 TCGA-44-8119 TCGA-49-4486 
       47.05         2.99        29.00        32.45         3.25        76.21 
TCGA-49-4505 TCGA-49-6744 TCGA-50-5049 TCGA-55-7725 TCGA-55-8089 TCGA-55-8506 
       14.07        29.26        70.55         1.28         3.29         0.36 
TCGA-55-A494 TCGA-62-8399 TCGA-62-A46U TCGA-64-5778 TCGA-67-6217 TCGA-69-7765 
       15.81        88.64        67.96        42.90        13.87         5.42 
TCGA-73-4670 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-86-8056 TCGA-86-8585 
        4.31        10.75        39.35       214.62         4.57         1.15 
TCGA-86-8673 TCGA-97-8171 TCGA-99-7458 TCGA-J2-8194 TCGA-L9-A444 TCGA-MN-A4N1 
       14.96        18.67        24.56        23.80         0.20        27.19 
TCGA-MP-A4TK 
       19.13 

$`COL7A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
       15.02         4.96        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 
        9.44        11.08        11.54        13.64        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        46.72        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       29.46        29.75        55.89        14.63        12.13        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       23.18         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       23.38        29.98        26.30        15.35         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       31.20         8.02        53.33        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       16.70        24.49         4.08        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 
       25.48         5.95         0.59         0.72        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        20.68        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        3.81        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  COL7A1 MUTATED COL7A1 WILD-TYPE 
             0.2              0.0 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
          214.62           223.96 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
           18.67            17.98 
[1] "0.2 - 214.6 (18.7)" "0.0 - 224.0 (18.0)"
[1] "hr=" "2.2"
D262V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL7A1 MUTATED         0        5        7         5         7          3
  COL7A1 WILD-TYPE       4      118      126        41        60         67
                  vv
clus               STAGE IIIB STAGE IV
  COL7A1 MUTATED            2        3
  COL7A1 WILD-TYPE          9       22
D262V3, multiclass
            clus
vv           COL7A1 MUTATED COL7A1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              118
  STAGE IB                7              126
  STAGE IIA               5               41
  STAGE IIB               7               60
  STAGE IIIA              3               67
  STAGE IIIB              2                9
  STAGE IV                3               22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL7A1 MUTATED     5  19   3   5
  COL7A1 WILD-TYPE 150 242  40  13
D262V4, multiclass
    clus
vv   COL7A1 MUTATED COL7A1 WILD-TYPE
  T1              5              150
  T2             19              242
  T3              3               40
  T4              5               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"
                  vv
clus                N0  N1 N2+N3
  COL7A1 MUTATED    19   8     4
  COL7A1 WILD-TYPE 288  81    68
D262V5, multiclass
       clus
vv      COL7A1 MUTATED COL7A1 WILD-TYPE
  N0                19              288
  N1                 8               81
  N2+N3              4               68
[1] 3 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
  COL7A1 MUTATED    21   2
  COL7A1 WILD-TYPE 306  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL7A1 MUTATED     21    2
  COL7A1 WILD-TYPE  306   21
   clus
vv  COL7A1 MUTATED COL7A1 WILD-TYPE
  0             21              306
  1              2               21
[1] 2 2
[1] FALSE
D262V7, binary
                  cls
clus                 0   1
  COL7A1 MUTATED    17  15
  COL7A1 WILD-TYPE 242 206
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL7A1 MUTATED     17   15
  COL7A1 WILD-TYPE  242  206
        clus
vv       COL7A1 MUTATED COL7A1 WILD-TYPE
  FEMALE             17              242
  MALE               15              206
[1] 2 2
[1] FALSE
D262V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL7A1 MUTATED                            0                                10
  COL7A1 WILD-TYPE                         18                                92
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL7A1 MUTATED                                                   15
  COL7A1 WILD-TYPE                                                279
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL7A1 MUTATED                                            1
  COL7A1 WILD-TYPE                                          3
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL7A1 MUTATED                                               3
  COL7A1 WILD-TYPE                                            16
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  COL7A1 MUTATED                                0
  COL7A1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  COL7A1 MUTATED                                    0
  COL7A1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL7A1 MUTATED                              0                             2
  COL7A1 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL7A1 MUTATED                                               1
  COL7A1 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  COL7A1 MUTATED                              0
  COL7A1 WILD-TYPE                            9
D262V9, multiclass
                                                    clus
vv                                                   COL7A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   3
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   COL7A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    16
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V10, binary
                  cls
clus                 0   1
  COL7A1 MUTATED     2  30
  COL7A1 WILD-TYPE  18 430
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL7A1 MUTATED      2   30
  COL7A1 WILD-TYPE   18  430
     clus
vv    COL7A1 MUTATED COL7A1 WILD-TYPE
  NO               2               18
  YES             30              430
[1] 2 2
[1] FALSE
D262V11, continuous
D262V12, continuous
                  vv
clus                R0  R1  R2  RX
  COL7A1 MUTATED    25   0   0   1
  COL7A1 WILD-TYPE 285  11   4  24
D262V13, multiclass
    clus
vv   COL7A1 MUTATED COL7A1 WILD-TYPE
  R0             25              285
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL7A1 MUTATED                                  0     1
  COL7A1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL7A1 MUTATED                           2    23
  COL7A1 WILD-TYPE                        27   354
D262V14, multiclass
                                  clus
vv                                 COL7A1 MUTATED COL7A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        23              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V15, binary
                  cls
clus                 0   1
  COL7A1 MUTATED     0  22
  COL7A1 WILD-TYPE   6 327
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL7A1 MUTATED      0   22
  COL7A1 WILD-TYPE    6  327
                        clus
vv                       COL7A1 MUTATED COL7A1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             22              327
[1] 2 2
[1] FALSE

Clustering(263) Variable = C1ORF105 MUTATION ANALYSIS
D263V1, survival
                    sevent
clus2                  0   1
  C1ORF105 MUTATED     1   3
  C1ORF105 WILD-TYPE 314 138
  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
                 4                452 
  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
                 3                138 
$`C1ORF105 MUTATED`
TCGA-05-5428 TCGA-64-5775 TCGA-78-7155 TCGA-78-8660 
       22.03         2.04        38.50        10.55 

$`C1ORF105 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       24.00        15.02        15.02         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       87.98        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
              2.04               0.00 
  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
             38.50             223.96 
  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
             16.29              18.03 
[1] "2.0 - 38.5 (16.3)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "3.3"
D263V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C1ORF105 MUTATED         0        0        1         1         1          1
  C1ORF105 WILD-TYPE       4      123      132        45        66         69
                    vv
clus                 STAGE IIIB STAGE IV
  C1ORF105 MUTATED            0        0
  C1ORF105 WILD-TYPE         11       25
D263V3, multiclass
            clus
vv           C1ORF105 MUTATED C1ORF105 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                123
  STAGE IB                  1                132
  STAGE IIA                 1                 45
  STAGE IIB                 1                 66
  STAGE IIIA                1                 69
  STAGE IIIB                0                 11
  STAGE IV                  0                 25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF105 MUTATED     1   2   0   1
  C1ORF105 WILD-TYPE 154 259  43  17
D263V4, multiclass
    clus
vv   C1ORF105 MUTATED C1ORF105 WILD-TYPE
  T1                1                154
  T2                2                259
  T3                0                 43
  T4                1                 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"
                    vv
clus                  N0  N1 N2+N3
  C1ORF105 MUTATED     2   2     0
  C1ORF105 WILD-TYPE 305  87    72
D263V5, multiclass
       clus
vv      C1ORF105 MUTATED C1ORF105 WILD-TYPE
  N0                   2                305
  N1                   2                 87
  N2+N3                0                 72
[1] 3 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
  C1ORF105 MUTATED     4   0
  C1ORF105 WILD-TYPE 323  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF105 MUTATED      4    0
  C1ORF105 WILD-TYPE  323   23
   clus
vv  C1ORF105 MUTATED C1ORF105 WILD-TYPE
  0                4                323
  1                0                 23
[1] 2 2
[1] FALSE
D263V7, binary
                    cls
clus                   0   1
  C1ORF105 MUTATED     0   4
  C1ORF105 WILD-TYPE 259 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF105 MUTATED      0    4
  C1ORF105 WILD-TYPE  259  217
        clus
vv       C1ORF105 MUTATED C1ORF105 WILD-TYPE
  FEMALE                0                259
  MALE                  4                217
[1] 2 2
[1] FALSE
D263V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  C1ORF105 MUTATED                            0
  C1ORF105 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  C1ORF105 MUTATED                                   1
  C1ORF105 WILD-TYPE                               101
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C1ORF105 MUTATED                                                    3
  C1ORF105 WILD-TYPE                                                291
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C1ORF105 MUTATED                                            0
  C1ORF105 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C1ORF105 MUTATED                                               0
  C1ORF105 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  C1ORF105 MUTATED                                0
  C1ORF105 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  C1ORF105 MUTATED                                    0
  C1ORF105 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C1ORF105 MUTATED                              0                             0
  C1ORF105 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C1ORF105 MUTATED                                               0
  C1ORF105 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  C1ORF105 MUTATED                              0
  C1ORF105 WILD-TYPE                            9
D263V9, multiclass
                                                    clus
vv                                                   C1ORF105 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   C1ORF105 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V10, binary
                    cls
clus                   0   1
  C1ORF105 MUTATED     0   4
  C1ORF105 WILD-TYPE  20 456
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF105 MUTATED      0    4
  C1ORF105 WILD-TYPE   20  456
     clus
vv    C1ORF105 MUTATED C1ORF105 WILD-TYPE
  NO                 0                 20
  YES                4                456
[1] 2 2
[1] FALSE
D263V11, continuous
D263V12, continuous
                    vv
clus                  R0  R1  R2  RX
  C1ORF105 MUTATED     4   0   0   0
  C1ORF105 WILD-TYPE 306  11   4  25
D263V13, multiclass
    clus
vv   C1ORF105 MUTATED C1ORF105 WILD-TYPE
  R0                4                306
  R1                0                 11
  R2                0                  4
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF105 MUTATED                                  0     0
  C1ORF105 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF105 MUTATED                           0     2
  C1ORF105 WILD-TYPE                        29   375
D263V14, multiclass
[1] "Remove cluster labels:" "C1ORF105 MUTATED"      
clus
  C1ORF105 MUTATED C1ORF105 WILD-TYPE 
                 2                412 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-38-4625         TCGA-38-4626         TCGA-38-4627 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-38-4628         TCGA-38-4629         TCGA-38-4630 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-38-4631         TCGA-38-4632         TCGA-38-6178 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-38-7271         TCGA-38-A44F         TCGA-44-2656 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-2657         TCGA-44-2661         TCGA-44-2665 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-3396         TCGA-44-3398         TCGA-44-3918 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-44-5643 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-5644         TCGA-44-5645         TCGA-44-6144 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-6145         TCGA-44-6146         TCGA-44-6147 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-6148         TCGA-44-6774         TCGA-44-6775 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-6776         TCGA-44-6777         TCGA-44-6778 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-6779         TCGA-44-7659         TCGA-44-7660 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-7661         TCGA-44-7662         TCGA-44-7667 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-7669         TCGA-44-7670         TCGA-44-7671 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-7672         TCGA-44-8117         TCGA-44-8119 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-8120         TCGA-44-A479         TCGA-44-A47A 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-A47B         TCGA-44-A47F         TCGA-44-A47G 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-44-A4SS         TCGA-44-A4SU         TCGA-49-4486 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-49-4487         TCGA-49-4488         TCGA-49-4490 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-49-4494         TCGA-49-4501         TCGA-49-4505 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-49-4506         TCGA-49-4507         TCGA-49-4510 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-49-4512         TCGA-49-4514         TCGA-49-6742 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-49-6743         TCGA-49-6744         TCGA-49-6745 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-49-6761         TCGA-49-6767         TCGA-50-5044 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-5045         TCGA-50-5049         TCGA-50-5051 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-5055         TCGA-50-5066         TCGA-50-5068 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-5072         TCGA-50-5930         TCGA-50-5931 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-5932         TCGA-50-5933         TCGA-50-5935 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-5936         TCGA-50-5939         TCGA-50-5941 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-5942         TCGA-50-5944         TCGA-50-5946 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-6590         TCGA-50-6591         TCGA-50-6592 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-6593         TCGA-50-6594         TCGA-50-6595 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-6597         TCGA-50-6673         TCGA-50-7109 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-50-8457         TCGA-50-8459         TCGA-50-8460 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-53-7624         TCGA-53-7626         TCGA-53-7813 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-1592         TCGA-55-1595 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-5899         TCGA-55-6543         TCGA-55-6642 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-6712         TCGA-55-6968         TCGA-55-6969 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-6970         TCGA-55-6971         TCGA-55-6972 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-6975         TCGA-55-6978         TCGA-55-6979 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-6980         TCGA-55-6981         TCGA-55-6982 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-6983         TCGA-55-6984         TCGA-55-6985 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-6986         TCGA-55-6987         TCGA-55-7227 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-7281         TCGA-55-7283         TCGA-55-7284 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-7570         TCGA-55-7573         TCGA-55-7574 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-7576         TCGA-55-7724         TCGA-55-7725 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-7726         TCGA-55-7727         TCGA-55-7816 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-7903         TCGA-55-7907         TCGA-55-7910 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-7911         TCGA-55-7914         TCGA-55-7994 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-7995         TCGA-55-8085         TCGA-55-8087 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8090         TCGA-55-8091 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8092         TCGA-55-8094         TCGA-55-8096 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8097         TCGA-55-8203         TCGA-55-8204 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8205         TCGA-55-8206         TCGA-55-8207 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8299         TCGA-55-8301 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8302         TCGA-55-8505         TCGA-55-8506 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8507         TCGA-55-8508         TCGA-55-8510 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8513 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8514         TCGA-55-8614         TCGA-55-8615 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8616         TCGA-55-8619         TCGA-55-8620 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-8621         TCGA-55-A48X         TCGA-55-A48Y 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-A48Z         TCGA-55-A490         TCGA-55-A491 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-A492         TCGA-55-A493         TCGA-55-A494 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-55-A4DF         TCGA-55-A4DG         TCGA-62-8394 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-62-8395         TCGA-62-8397         TCGA-62-8398 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-62-8399         TCGA-62-8402         TCGA-62-A46O 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-62-A46P         TCGA-62-A46R         TCGA-62-A46S 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-62-A46U         TCGA-62-A46V         TCGA-62-A46Y 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-62-A470         TCGA-62-A471         TCGA-62-A472 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1679 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-64-1681         TCGA-64-5774         TCGA-64-5778 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-64-5779         TCGA-64-5781         TCGA-64-5815 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-67-4679         TCGA-67-6215         TCGA-67-6216 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-67-6217         TCGA-69-7760         TCGA-69-7761 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-69-7763         TCGA-69-7764         TCGA-69-7765 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-69-7973         TCGA-69-7974         TCGA-69-7978 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-69-7979         TCGA-69-7980         TCGA-69-8253 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-69-8254         TCGA-69-8255         TCGA-69-A59K 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-71-6725         TCGA-71-8520         TCGA-73-4658 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-73-4659         TCGA-73-4662         TCGA-73-4666 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-73-4668         TCGA-73-4670         TCGA-73-4675 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-73-4676         TCGA-73-4677         TCGA-73-7498 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-73-7499         TCGA-78-7143         TCGA-78-7145 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7146         TCGA-78-7147         TCGA-78-7148 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7149         TCGA-78-7150         TCGA-78-7152 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7153         TCGA-78-7154         TCGA-78-7156 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7158         TCGA-78-7159         TCGA-78-7160 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7161         TCGA-78-7162         TCGA-78-7163 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7166         TCGA-78-7167         TCGA-78-7220 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7535         TCGA-78-7536         TCGA-78-7539 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-78-7540         TCGA-78-7542         TCGA-78-7633 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-83-5908         TCGA-86-6562         TCGA-86-6851 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-7701         TCGA-86-7711         TCGA-86-7713 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-7714         TCGA-86-7953         TCGA-86-7954 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-7955         TCGA-86-8054         TCGA-86-8055 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-8056         TCGA-86-8073         TCGA-86-8074 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-8075         TCGA-86-8076         TCGA-86-8278 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-8279         TCGA-86-8280         TCGA-86-8281 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-8358         TCGA-86-8359         TCGA-86-8585 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-8668         TCGA-86-8669         TCGA-86-8671 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-8672         TCGA-86-8673         TCGA-86-8674 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-A456         TCGA-86-A4JF         TCGA-86-A4P7 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-86-A4P8         TCGA-91-6828         TCGA-91-6829 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-91-6830         TCGA-91-6831         TCGA-91-6835 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-91-6836         TCGA-91-6840         TCGA-91-6847 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-91-6848         TCGA-91-6849         TCGA-91-7771 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-91-8496         TCGA-91-8497         TCGA-91-8499 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-91-A4BC         TCGA-91-A4BD         TCGA-93-7347 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-93-7348         TCGA-93-8067         TCGA-93-A4JN 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-93-A4JO         TCGA-93-A4JP         TCGA-93-A4JQ 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-95-7039         TCGA-95-7043         TCGA-95-7562 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-95-7567         TCGA-95-7944         TCGA-95-7947 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-95-7948         TCGA-95-8039         TCGA-95-8494 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-95-A4VK         TCGA-95-A4VN         TCGA-95-A4VP 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-7546         TCGA-97-7547         TCGA-97-7552 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-7553         TCGA-97-7554         TCGA-97-7937 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-7938         TCGA-97-7941         TCGA-97-8171 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-8172         TCGA-97-8174         TCGA-97-8175 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-8176         TCGA-97-8177         TCGA-97-8179 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-8552         TCGA-97-A4LX         TCGA-97-A4M0 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-A4M1         TCGA-97-A4M2         TCGA-97-A4M3 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-97-A4M5         TCGA-97-A4M6         TCGA-97-A4M7 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-99-7458         TCGA-99-8025         TCGA-99-8028 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-99-8032         TCGA-99-8033         TCGA-J2-8192 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-J2-8194         TCGA-J2-A4AD         TCGA-J2-A4AE 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-J2-A4AG         TCGA-L4-A4E5         TCGA-L4-A4E6 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-L9-A443         TCGA-L9-A444         TCGA-MN-A4N1 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-MN-A4N4         TCGA-MN-A4N5         TCGA-MP-A4SW 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-MP-A4SY         TCGA-MP-A4T2         TCGA-MP-A4T4 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-MP-A4T6         TCGA-MP-A4T9         TCGA-MP-A4TA 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-MP-A4TC         TCGA-MP-A4TD         TCGA-MP-A4TE 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-MP-A4TF         TCGA-MP-A4TH         TCGA-MP-A4TI 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-MP-A5C7         TCGA-NJ-A4YF         TCGA-NJ-A4YG 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-NJ-A4YI         TCGA-NJ-A4YP         TCGA-NJ-A4YQ 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-NJ-A55A         TCGA-NJ-A55O         TCGA-NJ-A55R 
"C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" "C1ORF105 WILD-TYPE" 
        TCGA-O1-A52J 
"C1ORF105 WILD-TYPE" 
D263V15, binary
                    cls
clus                   0   1
  C1ORF105 MUTATED     0   1
  C1ORF105 WILD-TYPE   6 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF105 MUTATED      0    1
  C1ORF105 WILD-TYPE    6  348
                        clus
vv                       C1ORF105 MUTATED C1ORF105 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                1                348
[1] 2 2
[1] FALSE

Clustering(264) Variable = NDUFB11 MUTATION ANALYSIS
D264V1, survival
                   sevent
clus2                 0   1
  NDUFB11 MUTATED     4   1
  NDUFB11 WILD-TYPE 311 140
  NDUFB11 MUTATED NDUFB11 WILD-TYPE 
                5               451 
  NDUFB11 MUTATED NDUFB11 WILD-TYPE 
                1               140 
$`NDUFB11 MUTATED`
TCGA-49-4490 TCGA-55-8205 TCGA-69-7974 TCGA-86-A4JF TCGA-97-7554 
       12.66         1.08         6.05        17.62        25.48 

$`NDUFB11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
        6.12        22.68        13.61         5.42         7.56         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        14.96        13.32        13.32        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  NDUFB11 MUTATED NDUFB11 WILD-TYPE 
             1.08              0.00 
  NDUFB11 MUTATED NDUFB11 WILD-TYPE 
            25.48            223.96 
  NDUFB11 MUTATED NDUFB11 WILD-TYPE 
            12.66             18.12 
[1] "1.1 - 25.5 (12.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.5"
D264V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NDUFB11 MUTATED         0        0        1         0         2          3
  NDUFB11 WILD-TYPE       4      123      132        46        65         67
                   vv
clus                STAGE IIIB STAGE IV
  NDUFB11 MUTATED            0        0
  NDUFB11 WILD-TYPE         11       25
D264V3, multiclass
            clus
vv           NDUFB11 MUTATED NDUFB11 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0               123
  STAGE IB                 1               132
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NDUFB11 MUTATED     0   4   2   0
  NDUFB11 WILD-TYPE 155 257  41  18
D264V4, multiclass
    clus
vv   NDUFB11 MUTATED NDUFB11 WILD-TYPE
  T1               0               155
  T2               4               257
  T3               2                41
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  NDUFB11 MUTATED     3   0     3
  NDUFB11 WILD-TYPE 304  89    69
D264V5, multiclass
       clus
vv      NDUFB11 MUTATED NDUFB11 WILD-TYPE
  N0                  3               304
  N1                  0                89
  N2+N3               3                69
[1] 3 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
  NDUFB11 MUTATED     4   0
  NDUFB11 WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFB11 MUTATED      4    0
  NDUFB11 WILD-TYPE  323   23
   clus
vv  NDUFB11 MUTATED NDUFB11 WILD-TYPE
  0               4               323
  1               0                23
[1] 2 2
[1] FALSE
D264V7, binary
                   cls
clus                  0   1
  NDUFB11 MUTATED     5   1
  NDUFB11 WILD-TYPE 254 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFB11 MUTATED      5    1
  NDUFB11 WILD-TYPE  254  220
        clus
vv       NDUFB11 MUTATED NDUFB11 WILD-TYPE
  FEMALE               5               254
  MALE                 1               220
[1] 2 2
[1] FALSE
D264V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  NDUFB11 MUTATED                            0
  NDUFB11 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  NDUFB11 MUTATED                                   1
  NDUFB11 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NDUFB11 MUTATED                                                    4
  NDUFB11 WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NDUFB11 MUTATED                                            0
  NDUFB11 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NDUFB11 MUTATED                                               0
  NDUFB11 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  NDUFB11 MUTATED                                0
  NDUFB11 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  NDUFB11 MUTATED                                    0
  NDUFB11 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NDUFB11 MUTATED                              0                             1
  NDUFB11 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NDUFB11 MUTATED                                               0
  NDUFB11 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  NDUFB11 MUTATED                              0
  NDUFB11 WILD-TYPE                            9
D264V9, multiclass
                                                    clus
vv                                                   NDUFB11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   NDUFB11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V10, binary
                   cls
clus                  0   1
  NDUFB11 MUTATED     1   5
  NDUFB11 WILD-TYPE  19 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFB11 MUTATED      1    5
  NDUFB11 WILD-TYPE   19  455
     clus
vv    NDUFB11 MUTATED NDUFB11 WILD-TYPE
  NO                1                19
  YES               5               455
[1] 2 2
[1] FALSE
D264V11, continuous
D264V12, continuous
                   vv
clus                 R0  R1  R2  RX
  NDUFB11 MUTATED     4   0   0   0
  NDUFB11 WILD-TYPE 306  11   4  25
D264V13, multiclass
    clus
vv   NDUFB11 MUTATED NDUFB11 WILD-TYPE
  R0               4               306
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NDUFB11 MUTATED                                  0     0
  NDUFB11 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NDUFB11 MUTATED                           0     6
  NDUFB11 WILD-TYPE                        29   371
D264V14, multiclass
                                  clus
vv                                 NDUFB11 MUTATED NDUFB11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V15, binary
                   cls
clus                  0   1
  NDUFB11 MUTATED     0   6
  NDUFB11 WILD-TYPE   6 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFB11 MUTATED      0    6
  NDUFB11 WILD-TYPE    6  343
                        clus
vv                       NDUFB11 MUTATED NDUFB11 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               6               343
[1] 2 2
[1] FALSE

Clustering(265) Variable = CHM MUTATION ANALYSIS
D265V1, survival
               sevent
clus2             0   1
  CHM MUTATED     9   4
  CHM WILD-TYPE 306 137
  CHM MUTATED CHM WILD-TYPE 
           13           443 
  CHM MUTATED CHM WILD-TYPE 
            4           137 
$`CHM MUTATED`
TCGA-44-7670 TCGA-44-8120 TCGA-44-A4SS TCGA-50-5931 TCGA-50-6590 TCGA-55-7995 
       29.00         8.55        13.64        14.27        42.35         0.16 
TCGA-55-8301 TCGA-62-A471 TCGA-64-5775 TCGA-69-7979 TCGA-73-4666 TCGA-78-8662 
        1.45        40.96         2.04         2.93        26.30       110.50 
TCGA-L4-A4E5 
       19.00 

$`CHM WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22         9.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
        0.53         6.48        17.65         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        23.38        29.98        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       35.47        16.44        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  CHM MUTATED CHM WILD-TYPE 
         0.16          0.00 
  CHM MUTATED CHM WILD-TYPE 
       110.50        223.96 
  CHM MUTATED CHM WILD-TYPE 
        14.27         18.08 
[1] "0.2 - 110.5 (14.3)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D265V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CHM MUTATED         1        2        6         2         1          2
  CHM WILD-TYPE       3      121      127        44        66         68
               vv
clus            STAGE IIIB STAGE IV
  CHM MUTATED            0        2
  CHM WILD-TYPE         11       23
D265V3, multiclass
            clus
vv           CHM MUTATED CHM WILD-TYPE
  STAGE I              1             3
  STAGE IA             2           121
  STAGE IB             6           127
  STAGE IIA            2            44
  STAGE IIB            1            66
  STAGE IIIA           2            68
  STAGE IIIB           0            11
  STAGE IV             2            23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CHM MUTATED     5  10   0   1
  CHM WILD-TYPE 150 251  43  17
D265V4, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  T1           5           150
  T2          10           251
  T3           0            43
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  CHM MUTATED    11   3     2
  CHM WILD-TYPE 296  86    70
D265V5, multiclass
       clus
vv      CHM MUTATED CHM WILD-TYPE
  N0             11           296
  N1              3            86
  N2+N3           2            70
[1] 3 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
  CHM MUTATED    12   2
  CHM WILD-TYPE 315  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED     12    2
  CHM WILD-TYPE  315   21
   clus
vv  CHM MUTATED CHM WILD-TYPE
  0          12           315
  1           2            21
[1] 2 2
[1] FALSE
D265V7, binary
               cls
clus              0   1
  CHM MUTATED    10   6
  CHM WILD-TYPE 249 215
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED     10    6
  CHM WILD-TYPE  249  215
        clus
vv       CHM MUTATED CHM WILD-TYPE
  FEMALE          10           249
  MALE             6           215
[1] 2 2
[1] FALSE
D265V8, continuous
[1] "Remove cluster labels:" "CHM MUTATED"           
clus
  CHM MUTATED CHM WILD-TYPE 
            2            82 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-62-A470    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681    TCGA-64-5778 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520    TCGA-73-4659 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-73-4662    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498    TCGA-73-7499 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711    TCGA-86-7713 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055    TCGA-86-8056 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278    TCGA-86-8279 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668    TCGA-86-8669 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849    TCGA-93-7348 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458    TCGA-MN-A4N1 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-MN-A4N4    TCGA-MN-A4N5 
"CHM WILD-TYPE" "CHM WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHM MUTATED                            1                                 0
  CHM WILD-TYPE                         17                               102
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHM MUTATED                                                   14
  CHM WILD-TYPE                                                280
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CHM MUTATED                                            0
  CHM WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CHM MUTATED                                               0
  CHM WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  CHM MUTATED                                0
  CHM WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  CHM MUTATED                                    1                            0
  CHM WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  CHM MUTATED                               0
  CHM WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CHM MUTATED                                               0
  CHM WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  CHM MUTATED                              0
  CHM WILD-TYPE                            9
D265V9, multiclass
                                                    clus
vv                                                   CHM MUTATED CHM WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            0           102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          14           280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           1             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V10, binary
               cls
clus              0   1
  CHM MUTATED     1  15
  CHM WILD-TYPE  19 445
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      1   15
  CHM WILD-TYPE   19  445
     clus
vv    CHM MUTATED CHM WILD-TYPE
  NO            1            19
  YES          15           445
[1] 2 2
[1] FALSE
D265V11, continuous
D265V12, continuous
               vv
clus             R0  R1  R2  RX
  CHM MUTATED    10   0   0   1
  CHM WILD-TYPE 300  11   4  24
D265V13, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  R0          10           300
  R1           0            11
  R2           0             4
  RX           1            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHM MUTATED                                  0     0
  CHM WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CHM MUTATED                           1    11
  CHM WILD-TYPE                        28   366
D265V14, multiclass
                                  clus
vv                                 CHM MUTATED CHM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     11           366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V15, binary
               cls
clus              0   1
  CHM MUTATED     1  11
  CHM WILD-TYPE   5 338
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      1   11
  CHM WILD-TYPE    5  338
                        clus
vv                       CHM MUTATED CHM WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          11           338
[1] 2 2
[1] FALSE

Clustering(266) Variable = TFDP1 MUTATION ANALYSIS
D266V1, survival
                 sevent
clus2               0   1
  TFDP1 MUTATED     6   1
  TFDP1 WILD-TYPE 309 140
  TFDP1 MUTATED TFDP1 WILD-TYPE 
              7             449 
  TFDP1 MUTATED TFDP1 WILD-TYPE 
              1             140 
$`TFDP1 MUTATED`
TCGA-44-2657 TCGA-44-7671 TCGA-50-5932 TCGA-55-A490 TCGA-55-A4DG TCGA-69-7979 
       13.15        17.59        40.60         1.58        19.99         2.93 
TCGA-97-8172 
       17.92 

$`TFDP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 
       44.61        14.73        26.30         4.37        46.98        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        29.00        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40        20.58        19.59         0.92        15.81        20.19 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.30        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  TFDP1 MUTATED TFDP1 WILD-TYPE 
           1.58            0.00 
  TFDP1 MUTATED TFDP1 WILD-TYPE 
          40.60          223.96 
  TFDP1 MUTATED TFDP1 WILD-TYPE 
          17.59           18.12 
[1] "1.6 - 40.6 (17.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D266V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TFDP1 MUTATED         0        1        4         1         1          0
  TFDP1 WILD-TYPE       4      122      129        45        66         70
                 vv
clus              STAGE IIIB STAGE IV
  TFDP1 MUTATED            0        0
  TFDP1 WILD-TYPE         11       25
D266V3, multiclass
            clus
vv           TFDP1 MUTATED TFDP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TFDP1 MUTATED     1   6   0   0
  TFDP1 WILD-TYPE 154 255  43  18
D266V4, multiclass
    clus
vv   TFDP1 MUTATED TFDP1 WILD-TYPE
  T1             1             154
  T2             6             255
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  TFDP1 MUTATED     5   1     0
  TFDP1 WILD-TYPE 302  88    72
D266V5, multiclass
       clus
vv      TFDP1 MUTATED TFDP1 WILD-TYPE
  N0                5             302
  N1                1              88
  N2+N3             0              72
[1] 3 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
  TFDP1 MUTATED     4   0
  TFDP1 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP1 MUTATED      4    0
  TFDP1 WILD-TYPE  323   23
   clus
vv  TFDP1 MUTATED TFDP1 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D266V7, binary
                 cls
clus                0   1
  TFDP1 MUTATED     3   4
  TFDP1 WILD-TYPE 256 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP1 MUTATED      3    4
  TFDP1 WILD-TYPE  256  217
        clus
vv       TFDP1 MUTATED TFDP1 WILD-TYPE
  FEMALE             3             256
  MALE               4             217
[1] 2 2
[1] FALSE
D266V8, continuous
[1] "Remove cluster labels:" "TFDP1 MUTATED"         
clus
  TFDP1 MUTATED TFDP1 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" "TFDP1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TFDP1 MUTATED                            2                                 1
  TFDP1 WILD-TYPE                         16                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TFDP1 MUTATED                                                    4
  TFDP1 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TFDP1 MUTATED                                            0
  TFDP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TFDP1 MUTATED                                               0
  TFDP1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TFDP1 MUTATED                                0
  TFDP1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TFDP1 MUTATED                                    0
  TFDP1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TFDP1 MUTATED                              0                             0
  TFDP1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TFDP1 MUTATED                                               0
  TFDP1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TFDP1 MUTATED                              0
  TFDP1 WILD-TYPE                            9
D266V9, multiclass
                                                    clus
vv                                                   TFDP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   TFDP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V10, binary
                 cls
clus                0   1
  TFDP1 MUTATED     0   7
  TFDP1 WILD-TYPE  20 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP1 MUTATED      0    7
  TFDP1 WILD-TYPE   20  453
     clus
vv    TFDP1 MUTATED TFDP1 WILD-TYPE
  NO              0              20
  YES             7             453
[1] 2 2
[1] FALSE
D266V11, continuous
D266V12, continuous
                 vv
clus               R0  R1  R2  RX
  TFDP1 MUTATED     3   0   0   0
  TFDP1 WILD-TYPE 307  11   4  25
D266V13, multiclass
    clus
vv   TFDP1 MUTATED TFDP1 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TFDP1 MUTATED                                  0     0
  TFDP1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TFDP1 MUTATED                           1     6
  TFDP1 WILD-TYPE                        28   371
D266V14, multiclass
                                  clus
vv                                 TFDP1 MUTATED TFDP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V15, binary
                 cls
clus                0   1
  TFDP1 MUTATED     0   7
  TFDP1 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP1 MUTATED      0    7
  TFDP1 WILD-TYPE    6  342
                        clus
vv                       TFDP1 MUTATED TFDP1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(267) Variable = NLGN2 MUTATION ANALYSIS
D267V1, survival
                 sevent
clus2               0   1
  NLGN2 MUTATED     5   4
  NLGN2 WILD-TYPE 310 137
  NLGN2 MUTATED NLGN2 WILD-TYPE 
              9             447 
  NLGN2 MUTATED NLGN2 WILD-TYPE 
              4             137 
$`NLGN2 MUTATED`
TCGA-05-4249 TCGA-35-4122 TCGA-50-6597 TCGA-55-7994 TCGA-55-8208 TCGA-64-5781 
       50.07         7.40        41.69        19.82        22.16        51.25 
TCGA-78-7542 TCGA-MP-A4T4 TCGA-MP-A4TK 
       10.55        86.04        19.13 

$`NLGN2 WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
       10.09        29.46        11.05        14.66        14.10        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  NLGN2 MUTATED NLGN2 WILD-TYPE 
            7.4             0.0 
  NLGN2 MUTATED NLGN2 WILD-TYPE 
          86.04          223.96 
  NLGN2 MUTATED NLGN2 WILD-TYPE 
          22.16           17.75 
[1] "7.4 - 86.0 (22.2)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.1"
D267V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NLGN2 MUTATED         0        2        4         0         3          0
  NLGN2 WILD-TYPE       4      121      129        46        64         70
                 vv
clus              STAGE IIIB STAGE IV
  NLGN2 MUTATED            0        0
  NLGN2 WILD-TYPE         11       25
D267V3, multiclass
            clus
vv           NLGN2 MUTATED NLGN2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              3              64
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLGN2 MUTATED     2   6   1   0
  NLGN2 WILD-TYPE 153 255  42  18
D267V4, multiclass
    clus
vv   NLGN2 MUTATED NLGN2 WILD-TYPE
  T1             2             153
  T2             6             255
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  NLGN2 MUTATED     7   2     0
  NLGN2 WILD-TYPE 300  87    72
D267V5, multiclass
       clus
vv      NLGN2 MUTATED NLGN2 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             0              72
[1] 3 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
  NLGN2 MUTATED     7   0
  NLGN2 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLGN2 MUTATED      7    0
  NLGN2 WILD-TYPE  320   23
   clus
vv  NLGN2 MUTATED NLGN2 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D267V7, binary
                 cls
clus                0   1
  NLGN2 MUTATED     5   4
  NLGN2 WILD-TYPE 254 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLGN2 MUTATED      5    4
  NLGN2 WILD-TYPE  254  217
        clus
vv       NLGN2 MUTATED NLGN2 WILD-TYPE
  FEMALE             5             254
  MALE               4             217
[1] 2 2
[1] FALSE
D267V8, continuous
[1] "Remove cluster labels:" "NLGN2 MUTATED"         
clus
  NLGN2 MUTATED NLGN2 WILD-TYPE 
              2              82 
     TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ      TCGA-55-7283 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8507 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-55-8508      TCGA-55-8511      TCGA-55-8512      TCGA-55-8619 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"NLGN2 WILD-TYPE" "NLGN2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NLGN2 MUTATED                            0                                 1
  NLGN2 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NLGN2 MUTATED                                                    8
  NLGN2 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NLGN2 MUTATED                                            0
  NLGN2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NLGN2 MUTATED                                               0
  NLGN2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NLGN2 MUTATED                                0
  NLGN2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NLGN2 MUTATED                                    0
  NLGN2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NLGN2 MUTATED                              0                             0
  NLGN2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NLGN2 MUTATED                                               0
  NLGN2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NLGN2 MUTATED                              0
  NLGN2 WILD-TYPE                            9
D267V9, multiclass
                                                    clus
vv                                                   NLGN2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NLGN2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V10, binary
                 cls
clus                0   1
  NLGN2 MUTATED     0   9
  NLGN2 WILD-TYPE  20 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLGN2 MUTATED      0    9
  NLGN2 WILD-TYPE   20  451
     clus
vv    NLGN2 MUTATED NLGN2 WILD-TYPE
  NO              0              20
  YES             9             451
[1] 2 2
[1] FALSE
D267V11, continuous
D267V12, continuous
                 vv
clus               R0  R1  R2  RX
  NLGN2 MUTATED     9   0   0   0
  NLGN2 WILD-TYPE 301  11   4  25
D267V13, multiclass
    clus
vv   NLGN2 MUTATED NLGN2 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLGN2 MUTATED                                  0     0
  NLGN2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NLGN2 MUTATED                           0     7
  NLGN2 WILD-TYPE                        29   370
D267V14, multiclass
                                  clus
vv                                 NLGN2 MUTATED NLGN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V15, binary
                 cls
clus                0   1
  NLGN2 MUTATED     0   5
  NLGN2 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLGN2 MUTATED      0    5
  NLGN2 WILD-TYPE    6  344
                        clus
vv                       NLGN2 MUTATED NLGN2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(268) Variable = PLEKHG5 MUTATION ANALYSIS
D268V1, survival
                   sevent
clus2                 0   1
  PLEKHG5 MUTATED     7   0
  PLEKHG5 WILD-TYPE 308 141
  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
                7               449 
  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
                0               141 
$`PLEKHG5 MUTATED`
TCGA-05-5428 TCGA-55-6712 TCGA-55-7574 TCGA-55-8089 TCGA-69-7974 TCGA-86-8073 
       22.03         0.79         3.12         3.29         6.05        24.33 
TCGA-91-6848 
        7.36 

$`PLEKHG5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       24.00        15.02        15.02         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
        0.59         1.15         7.99         0.20         0.13         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
             0.79              0.00 
  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
            24.33            223.96 
  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
             6.05             18.12 
[1] "0.8 - 24.3 (6.0)"   "0.0 - 224.0 (18.1)"
[1] "hr="     "3300000"
D268V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PLEKHG5 MUTATED         0        1        2         2         0          2
  PLEKHG5 WILD-TYPE       4      122      131        44        67         68
                   vv
clus                STAGE IIIB STAGE IV
  PLEKHG5 MUTATED            0        0
  PLEKHG5 WILD-TYPE         11       25
D268V3, multiclass
            clus
vv           PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 2               131
  STAGE IIA                2                44
  STAGE IIB                0                67
  STAGE IIIA               2                68
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHG5 MUTATED     2   5   0   0
  PLEKHG5 WILD-TYPE 153 256  43  18
D268V4, multiclass
    clus
vv   PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  T1               2               153
  T2               5               256
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  PLEKHG5 MUTATED     3   2     2
  PLEKHG5 WILD-TYPE 304  87    70
D268V5, multiclass
       clus
vv      PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  N0                  3               304
  N1                  2                87
  N2+N3               2                70
[1] 3 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
  PLEKHG5 MUTATED     4   0
  PLEKHG5 WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG5 MUTATED      4    0
  PLEKHG5 WILD-TYPE  323   23
   clus
vv  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  0               4               323
  1               0                23
[1] 2 2
[1] FALSE
D268V7, binary
                   cls
clus                  0   1
  PLEKHG5 MUTATED     2   5
  PLEKHG5 WILD-TYPE 257 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG5 MUTATED      2    5
  PLEKHG5 WILD-TYPE  257  216
        clus
vv       PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  FEMALE               2               257
  MALE                 5               216
[1] 2 2
[1] FALSE
D268V8, continuous
[1] "Remove cluster labels:" "PLEKHG5 MUTATED"       
clus
  PLEKHG5 MUTATED PLEKHG5 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8096        TCGA-55-8205        TCGA-55-8208 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8511        TCGA-55-8512 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-69-8254        TCGA-71-6725        TCGA-71-8520        TCGA-73-4659 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-73-4662        TCGA-73-4666        TCGA-73-4668        TCGA-73-4676 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-73-7498        TCGA-73-7499        TCGA-75-5122        TCGA-83-5908 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-86-7701        TCGA-86-7711        TCGA-86-7713        TCGA-86-7714 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-86-7954        TCGA-86-7955        TCGA-86-8055        TCGA-86-8056 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-86-8074        TCGA-86-8075        TCGA-86-8076        TCGA-86-8278 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8281        TCGA-86-8358        TCGA-86-8359 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-86-8668        TCGA-86-8669        TCGA-86-8671        TCGA-86-A4JF 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"PLEKHG5 WILD-TYPE" "PLEKHG5 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PLEKHG5 MUTATED                            0
  PLEKHG5 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PLEKHG5 MUTATED                                   2
  PLEKHG5 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PLEKHG5 MUTATED                                                    4
  PLEKHG5 WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PLEKHG5 MUTATED                                            0
  PLEKHG5 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PLEKHG5 MUTATED                                               1
  PLEKHG5 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  PLEKHG5 MUTATED                                0
  PLEKHG5 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  PLEKHG5 MUTATED                                    0
  PLEKHG5 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PLEKHG5 MUTATED                              0                             0
  PLEKHG5 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PLEKHG5 MUTATED                                               0
  PLEKHG5 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  PLEKHG5 MUTATED                              0
  PLEKHG5 WILD-TYPE                            9
D268V9, multiclass
                                                    clus
vv                                                   PLEKHG5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   PLEKHG5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V10, binary
                   cls
clus                  0   1
  PLEKHG5 MUTATED     2   5
  PLEKHG5 WILD-TYPE  18 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG5 MUTATED      2    5
  PLEKHG5 WILD-TYPE   18  455
     clus
vv    PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  NO                2                18
  YES               5               455
[1] 2 2
[1] FALSE
D268V11, continuous
D268V12, continuous
                   vv
clus                 R0  R1  R2  RX
  PLEKHG5 MUTATED     3   1   0   0
  PLEKHG5 WILD-TYPE 307  10   4  25
D268V13, multiclass
    clus
vv   PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  R0               3               307
  R1               1                10
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHG5 MUTATED                                  0     0
  PLEKHG5 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHG5 MUTATED                           0     6
  PLEKHG5 WILD-TYPE                        29   371
D268V14, multiclass
                                  clus
vv                                 PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V15, binary
                   cls
clus                  0   1
  PLEKHG5 MUTATED     0   5
  PLEKHG5 WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG5 MUTATED      0    5
  PLEKHG5 WILD-TYPE    6  344
                        clus
vv                       PLEKHG5 MUTATED PLEKHG5 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(269) Variable = OR5P3 MUTATION ANALYSIS
D269V1, survival
                 sevent
clus2               0   1
  OR5P3 MUTATED     2   1
  OR5P3 WILD-TYPE 313 140
  OR5P3 MUTATED OR5P3 WILD-TYPE 
              3             453 
  OR5P3 MUTATED OR5P3 WILD-TYPE 
              1             140 
$`OR5P3 MUTATED`
TCGA-05-4396 TCGA-55-8514 TCGA-64-5781 
        9.96         6.64        51.25 

$`OR5P3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
        0.49        17.72         0.30         0.10         4.80        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  OR5P3 MUTATED OR5P3 WILD-TYPE 
           6.64            0.00 
  OR5P3 MUTATED OR5P3 WILD-TYPE 
          51.25          223.96 
  OR5P3 MUTATED OR5P3 WILD-TYPE 
           9.96           18.08 
[1] "6.6 - 51.2 (10.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D269V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  OR5P3 MUTATED         0        0        2         0         0          0
  OR5P3 WILD-TYPE       4      123      131        46        67         70
                 vv
clus              STAGE IIIB STAGE IV
  OR5P3 MUTATED            1        0
  OR5P3 WILD-TYPE         10       25
D269V3, multiclass
            clus
vv           OR5P3 MUTATED OR5P3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               2             131
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5P3 MUTATED     0   2   0   1
  OR5P3 WILD-TYPE 155 259  43  17
D269V4, multiclass
    clus
vv   OR5P3 MUTATED OR5P3 WILD-TYPE
  T1             0             155
  T2             2             259
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  OR5P3 MUTATED     2   1     0
  OR5P3 WILD-TYPE 305  88    72
D269V5, multiclass
       clus
vv      OR5P3 MUTATED OR5P3 WILD-TYPE
  N0                2             305
  N1                1              88
  N2+N3             0              72
[1] 3 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
  OR5P3 MUTATED     2   0
  OR5P3 WILD-TYPE 325  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5P3 MUTATED      2    0
  OR5P3 WILD-TYPE  325   23
   clus
vv  OR5P3 MUTATED OR5P3 WILD-TYPE
  0             2             325
  1             0              23
[1] 2 2
[1] FALSE
D269V7, binary
                 cls
clus                0   1
  OR5P3 MUTATED     2   1
  OR5P3 WILD-TYPE 257 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5P3 MUTATED      2    1
  OR5P3 WILD-TYPE  257  220
        clus
vv       OR5P3 MUTATED OR5P3 WILD-TYPE
  FEMALE             2             257
  MALE               1             220
[1] 2 2
[1] FALSE
D269V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  OR5P3 MUTATED                            0                                 2
  OR5P3 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  OR5P3 MUTATED                                                    1
  OR5P3 WILD-TYPE                                                293
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  OR5P3 MUTATED                                            0
  OR5P3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  OR5P3 MUTATED                                               0
  OR5P3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  OR5P3 MUTATED                                0
  OR5P3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  OR5P3 MUTATED                                    0
  OR5P3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  OR5P3 MUTATED                              0                             0
  OR5P3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  OR5P3 MUTATED                                               0
  OR5P3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  OR5P3 MUTATED                              0
  OR5P3 WILD-TYPE                            9
D269V9, multiclass
                                                    clus
vv                                                   OR5P3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   OR5P3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V10, binary
                 cls
clus                0   1
  OR5P3 MUTATED     0   3
  OR5P3 WILD-TYPE  20 457
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5P3 MUTATED      0    3
  OR5P3 WILD-TYPE   20  457
     clus
vv    OR5P3 MUTATED OR5P3 WILD-TYPE
  NO              0              20
  YES             3             457
[1] 2 2
[1] FALSE
D269V11, continuous
D269V12, continuous
                 vv
clus               R0  R1  R2  RX
  OR5P3 MUTATED     3   0   0   0
  OR5P3 WILD-TYPE 307  11   4  25
D269V13, multiclass
    clus
vv   OR5P3 MUTATED OR5P3 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5P3 MUTATED                                  0     0
  OR5P3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5P3 MUTATED                           1     1
  OR5P3 WILD-TYPE                        28   376
D269V14, multiclass
[1] "Remove cluster labels:" "OR5P3 MUTATED"         
clus
  OR5P3 MUTATED OR5P3 WILD-TYPE 
              2             412 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-38-4625 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-38-4626      TCGA-38-4627      TCGA-38-4628      TCGA-38-4629 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-38-4630      TCGA-38-4631      TCGA-38-4632      TCGA-38-6178 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-2661      TCGA-44-2665      TCGA-44-3396      TCGA-44-3398 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-3919      TCGA-44-4112      TCGA-44-5643 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-5644      TCGA-44-5645      TCGA-44-6144      TCGA-44-6145 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-6146      TCGA-44-6147      TCGA-44-6148      TCGA-44-6774 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-6776      TCGA-44-6777      TCGA-44-6778 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-6779      TCGA-44-7659      TCGA-44-7660      TCGA-44-7661 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-7662      TCGA-44-7667      TCGA-44-7669      TCGA-44-7670 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-7671      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4488      TCGA-49-4490 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4501      TCGA-49-4505      TCGA-49-4506 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-49-4507      TCGA-49-4510      TCGA-49-4512      TCGA-49-4514 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-49-6745 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-49-6761      TCGA-49-6767      TCGA-50-5044      TCGA-50-5045 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-5049      TCGA-50-5051      TCGA-50-5055      TCGA-50-5066 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-5068      TCGA-50-5072      TCGA-50-5930      TCGA-50-5931 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-5932      TCGA-50-5933      TCGA-50-5935      TCGA-50-5936 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-5939      TCGA-50-5941      TCGA-50-5942      TCGA-50-5944 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-5946      TCGA-50-6590      TCGA-50-6591      TCGA-50-6592 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-6593      TCGA-50-6594      TCGA-50-6595      TCGA-50-6597 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-6673      TCGA-50-7109      TCGA-50-8457      TCGA-50-8459 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-50-8460      TCGA-53-7624      TCGA-53-7626      TCGA-53-7813 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-1592      TCGA-55-1595      TCGA-55-5899 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-6543      TCGA-55-6642      TCGA-55-6712      TCGA-55-6968 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-6969      TCGA-55-6970      TCGA-55-6971      TCGA-55-6972 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-6975      TCGA-55-6978      TCGA-55-6979      TCGA-55-6980 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-6981      TCGA-55-6982      TCGA-55-6983      TCGA-55-6984 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-6985      TCGA-55-6986      TCGA-55-6987      TCGA-55-7227 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-7281      TCGA-55-7283      TCGA-55-7284      TCGA-55-7570 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7727      TCGA-55-7816 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-7903      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-7994      TCGA-55-7995      TCGA-55-8085 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8087      TCGA-55-8089      TCGA-55-8090      TCGA-55-8091 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8203      TCGA-55-8204      TCGA-55-8205      TCGA-55-8206 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8207      TCGA-55-8208      TCGA-55-8299      TCGA-55-8301 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8302      TCGA-55-8505      TCGA-55-8506      TCGA-55-8507 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8508      TCGA-55-8510      TCGA-55-8511      TCGA-55-8512 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8513      TCGA-55-8614      TCGA-55-8615      TCGA-55-8616 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-55-A4DG      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1676      TCGA-64-1677      TCGA-64-1679 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5774      TCGA-64-5775      TCGA-64-5778 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-64-5779      TCGA-64-5815      TCGA-67-3771      TCGA-67-3772 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-67-3773      TCGA-67-4679      TCGA-67-6215      TCGA-67-6216 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-67-6217      TCGA-69-7760      TCGA-69-7761      TCGA-69-7763 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-69-7764      TCGA-69-7765      TCGA-69-7973      TCGA-69-7974 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-69-7978      TCGA-69-7979      TCGA-69-7980      TCGA-69-8253 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-69-8254      TCGA-69-8255      TCGA-69-A59K      TCGA-71-6725 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4658      TCGA-73-4659      TCGA-73-4662 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4668      TCGA-73-4670      TCGA-73-4675 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-4677      TCGA-73-7498      TCGA-73-7499 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-78-7143      TCGA-78-7145      TCGA-78-7146      TCGA-78-7147 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-78-7148      TCGA-78-7149      TCGA-78-7150      TCGA-78-7152 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-78-7153      TCGA-78-7154      TCGA-78-7155      TCGA-78-7156 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-78-7158      TCGA-78-7159      TCGA-78-7160      TCGA-78-7161 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-78-7162      TCGA-78-7163      TCGA-78-7166      TCGA-78-7167 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-78-7220      TCGA-78-7535      TCGA-78-7536      TCGA-78-7539 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-78-7540      TCGA-78-7542      TCGA-78-7633      TCGA-83-5908 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7953      TCGA-86-7954 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-7955      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8280      TCGA-86-8281 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8585      TCGA-86-8668 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8671      TCGA-86-8672      TCGA-86-8673 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-86-A4P8      TCGA-91-6828      TCGA-91-6829      TCGA-91-6830 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-91-6831      TCGA-91-6835      TCGA-91-6836      TCGA-91-6840 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-91-6847      TCGA-91-6848      TCGA-91-6849      TCGA-91-7771 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-91-8496      TCGA-91-8497      TCGA-91-8499      TCGA-91-A4BC 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-91-A4BD      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JP      TCGA-93-A4JQ 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-95-7039      TCGA-95-7043      TCGA-95-7562      TCGA-95-7567 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-95-7944      TCGA-95-7947      TCGA-95-7948      TCGA-95-8039 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-95-8494      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7547      TCGA-97-7552      TCGA-97-7553 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-97-7554      TCGA-97-7937      TCGA-97-7938      TCGA-97-7941 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8175 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-97-8176      TCGA-97-8177      TCGA-97-8179      TCGA-97-8552 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M6      TCGA-97-A4M7 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-99-8033      TCGA-J2-8192      TCGA-J2-8194      TCGA-J2-A4AD 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-J2-A4AE      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SW      TCGA-MP-A4SY      TCGA-MP-A4T2 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T9      TCGA-MP-A4TA 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-MP-A4TC      TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TF 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A5C7      TCGA-NJ-A4YF 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
     TCGA-NJ-A55A      TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" "OR5P3 WILD-TYPE" 
D269V15, binary
                 cls
clus                0   1
  OR5P3 MUTATED     0   2
  OR5P3 WILD-TYPE   6 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5P3 MUTATED      0    2
  OR5P3 WILD-TYPE    6  347
                        clus
vv                       OR5P3 MUTATED OR5P3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2             347
[1] 2 2
[1] FALSE

Clustering(270) Variable = CHD5 MUTATION ANALYSIS
D270V1, survival
                sevent
clus2              0   1
  CHD5 MUTATED    16  13
  CHD5 WILD-TYPE 299 128
  CHD5 MUTATED CHD5 WILD-TYPE 
            29            427 
  CHD5 MUTATED CHD5 WILD-TYPE 
            13            128 
$`CHD5 MUTATED`
TCGA-05-4390 TCGA-05-5423 TCGA-38-4631 TCGA-44-3918 TCGA-50-5045 TCGA-50-5930 
       37.02         4.96        11.64        34.06        71.47         9.27 
TCGA-50-5939 TCGA-50-6590 TCGA-53-7624 TCGA-55-7727 TCGA-55-8299 TCGA-55-8301 
       15.12        42.35        34.29         1.12        15.42         1.45 
TCGA-64-1681 TCGA-69-7765 TCGA-69-7973 TCGA-78-7155 TCGA-78-8640 TCGA-78-8662 
       38.37         5.42         7.56        38.50       214.62       110.50 
TCGA-86-8073 TCGA-91-6831 TCGA-95-7947 TCGA-99-8025 TCGA-L9-A443 TCGA-L9-A444 
       24.33        10.19        15.68        34.85         3.81         0.20 
TCGA-MP-A4T4 TCGA-MP-A4TC TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YP 
       86.04         2.43        19.13        71.05         1.64 

$`CHD5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        8.22        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       25.61         7.59        27.25        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       23.18         1.28         1.28         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        1.51         2.17        22.16         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 TCGA-69-7978 
        6.64         6.12        22.68        13.61         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        10.55        32.68        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
       10.09        29.46        11.05        14.66        14.10        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CHD5 MUTATED CHD5 WILD-TYPE 
           0.2            0.0 
  CHD5 MUTATED CHD5 WILD-TYPE 
        214.62         223.96 
  CHD5 MUTATED CHD5 WILD-TYPE 
         15.68          18.08 
[1] "0.2 - 214.6 (15.7)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D270V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CHD5 MUTATED         0        8       12         1         3          4
  CHD5 WILD-TYPE       4      115      121        45        64         66
                vv
clus             STAGE IIIB STAGE IV
  CHD5 MUTATED            0        2
  CHD5 WILD-TYPE         11       23
D270V3, multiclass
            clus
vv           CHD5 MUTATED CHD5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              8            115
  STAGE IB             12            121
  STAGE IIA             1             45
  STAGE IIB             3             64
  STAGE IIIA            4             66
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD5 MUTATED    10  18   1   1
  CHD5 WILD-TYPE 145 243  42  17
D270V4, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  T1           10            145
  T2           18            243
  T3            1             42
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  CHD5 MUTATED    21   5     4
  CHD5 WILD-TYPE 286  84    68
D270V5, multiclass
       clus
vv      CHD5 MUTATED CHD5 WILD-TYPE
  N0              21            286
  N1               5             84
  N2+N3            4             68
[1] 3 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
  CHD5 MUTATED    21   1
  CHD5 WILD-TYPE 306  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     21    1
  CHD5 WILD-TYPE  306   22
   clus
vv  CHD5 MUTATED CHD5 WILD-TYPE
  0           21            306
  1            1             22
[1] 2 2
[1] FALSE
D270V7, binary
                cls
clus               0   1
  CHD5 MUTATED    17  13
  CHD5 WILD-TYPE 242 208
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     17   13
  CHD5 WILD-TYPE  242  208
        clus
vv       CHD5 MUTATED CHD5 WILD-TYPE
  FEMALE           17            242
  MALE             13            208
[1] 2 2
[1] FALSE
D270V8, continuous
[1] "Remove cluster labels:" "CHD5 MUTATED"          
clus
  CHD5 MUTATED CHD5 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-5778 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"CHD5 WILD-TYPE" "CHD5 WILD-TYPE" "CHD5 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHD5 MUTATED                            0                                 8
  CHD5 WILD-TYPE                         18                                94
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHD5 MUTATED                                                   20
  CHD5 WILD-TYPE                                                274
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CHD5 MUTATED                                            0
  CHD5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CHD5 MUTATED                                               1
  CHD5 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  CHD5 MUTATED                                0
  CHD5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  CHD5 MUTATED                                    0
  CHD5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CHD5 MUTATED                              0                             1
  CHD5 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CHD5 MUTATED                                               0
  CHD5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  CHD5 MUTATED                              0
  CHD5 WILD-TYPE                            9
D270V9, multiclass
                                                    clus
vv                                                   CHD5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           20
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   CHD5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            274
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V10, binary
                cls
clus               0   1
  CHD5 MUTATED     2  28
  CHD5 WILD-TYPE  18 432
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED      2   28
  CHD5 WILD-TYPE   18  432
     clus
vv    CHD5 MUTATED CHD5 WILD-TYPE
  NO             2             18
  YES           28            432
[1] 2 2
[1] FALSE
D270V11, continuous
D270V12, continuous
                vv
clus              R0  R1  R2  RX
  CHD5 MUTATED    21   0   0   0
  CHD5 WILD-TYPE 289  11   4  25
D270V13, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  R0           21            289
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD5 MUTATED                                  0     0
  CHD5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD5 MUTATED                           4    20
  CHD5 WILD-TYPE                        25   357
D270V14, multiclass
                                  clus
vv                                 CHD5 MUTATED CHD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   4             25
  WHITE                                      20            357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V15, binary
                cls
clus               0   1
  CHD5 MUTATED     1  21
  CHD5 WILD-TYPE   5 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED      1   21
  CHD5 WILD-TYPE    5  328
                        clus
vv                       CHD5 MUTATED CHD5 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           21            328
[1] 2 2
[1] FALSE

Clustering(271) Variable = FBXO34 MUTATION ANALYSIS
D271V1, survival
                  sevent
clus2                0   1
  FBXO34 MUTATED     4   2
  FBXO34 WILD-TYPE 311 139
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               6              450 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               2              139 
$`FBXO34 MUTATED`
TCGA-49-4488 TCGA-55-7903 TCGA-55-7995 TCGA-55-8302 TCGA-69-7979 TCGA-78-7155 
       28.57        18.64         0.16         0.76         2.93        38.50 

$`FBXO34 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15        19.82        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.30        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  FBXO34 MUTATED FBXO34 WILD-TYPE 
            0.16             0.00 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
           38.50           223.96 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
          10.785           18.030 
[1] "0.2 - 38.5 (10.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.8"
D271V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FBXO34 MUTATED         0        3        3         0         0          0
  FBXO34 WILD-TYPE       4      120      130        46        67         70
                  vv
clus               STAGE IIIB STAGE IV
  FBXO34 MUTATED            0        0
  FBXO34 WILD-TYPE         11       25
D271V3, multiclass
            clus
vv           FBXO34 MUTATED FBXO34 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                3              130
  STAGE IIA               0               46
  STAGE IIB               0               67
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     3   3   0   0
  FBXO34 WILD-TYPE 152 258  43  18
D271V4, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  T1              3              152
  T2              3              258
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  FBXO34 MUTATED     6   0     0
  FBXO34 WILD-TYPE 301  89    72
D271V5, multiclass
       clus
vv      FBXO34 MUTATED FBXO34 WILD-TYPE
  N0                 6              301
  N1                 0               89
  N2+N3              0               72
[1] 3 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
  FBXO34 MUTATED     2   0
  FBXO34 WILD-TYPE 325  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      2    0
  FBXO34 WILD-TYPE  325   23
   clus
vv  FBXO34 MUTATED FBXO34 WILD-TYPE
  0              2              325
  1              0               23
[1] 2 2
[1] FALSE
D271V7, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     3   3
  FBXO34 WILD-TYPE 256 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      3    3
  FBXO34 WILD-TYPE  256  218
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  FEMALE              3              256
  MALE                3              218
[1] 2 2
[1] FALSE
D271V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FBXO34 MUTATED                            1                                 0
  FBXO34 WILD-TYPE                         17                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FBXO34 MUTATED                                                    5
  FBXO34 WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FBXO34 MUTATED                                            0
  FBXO34 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FBXO34 MUTATED                                               0
  FBXO34 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  FBXO34 MUTATED                                0
  FBXO34 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  FBXO34 MUTATED                                    0
  FBXO34 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FBXO34 MUTATED                              0                             0
  FBXO34 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FBXO34 MUTATED                                               0
  FBXO34 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  FBXO34 MUTATED                              0
  FBXO34 WILD-TYPE                            9
D271V9, multiclass
                                                    clus
vv                                                   FBXO34 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   FBXO34 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V10, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     0   6
  FBXO34 WILD-TYPE  20 454
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      0    6
  FBXO34 WILD-TYPE   20  454
     clus
vv    FBXO34 MUTATED FBXO34 WILD-TYPE
  NO               0               20
  YES              6              454
[1] 2 2
[1] FALSE
D271V11, continuous
D271V12, continuous
                  vv
clus                R0  R1  R2  RX
  FBXO34 MUTATED     5   0   0   0
  FBXO34 WILD-TYPE 305  11   4  25
D271V13, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  R0              5              305
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO34 MUTATED                                  0     0
  FBXO34 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO34 MUTATED                           0     6
  FBXO34 WILD-TYPE                        29   371
D271V14, multiclass
                                  clus
vv                                 FBXO34 MUTATED FBXO34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         6              371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V15, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     0   4
  FBXO34 WILD-TYPE   6 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      0    4
  FBXO34 WILD-TYPE    6  345
                        clus
vv                       FBXO34 MUTATED FBXO34 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(272) Variable = TXLNB MUTATION ANALYSIS
D272V1, survival
                 sevent
clus2               0   1
  TXLNB MUTATED    12   4
  TXLNB WILD-TYPE 303 137
  TXLNB MUTATED TXLNB WILD-TYPE 
             16             440 
  TXLNB MUTATED TXLNB WILD-TYPE 
              4             137 
$`TXLNB MUTATED`
TCGA-38-4631 TCGA-44-7667 TCGA-44-7672 TCGA-44-8119 TCGA-50-6593 TCGA-55-8208 
       11.64        36.07        23.64         3.25        11.05        22.16 
TCGA-55-A493 TCGA-64-1676 TCGA-73-4659 TCGA-86-7713 TCGA-86-8073 TCGA-86-8585 
        0.92        56.81        23.38        13.87        24.33         1.15 
TCGA-86-A4JF TCGA-95-7947 TCGA-97-8172 TCGA-MP-A4T4 
       17.62        15.68        17.92        86.04 

$`TXLNB WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       18.87        29.00        17.59        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       22.55        42.35         3.91        25.55        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       19.59        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 
        7.04         2.01         0.10        52.60        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        34.39        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       16.70        24.49         4.08         4.57         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
        5.95         0.59         0.72        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  TXLNB MUTATED TXLNB WILD-TYPE 
           0.92            0.00 
  TXLNB MUTATED TXLNB WILD-TYPE 
          86.04          223.96 
  TXLNB MUTATED TXLNB WILD-TYPE 
          17.77           18.10 
[1] "0.9 - 86.0 (17.8)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D272V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TXLNB MUTATED         0        4        6         1         4          2
  TXLNB WILD-TYPE       4      119      127        45        63         68
                 vv
clus              STAGE IIIB STAGE IV
  TXLNB MUTATED            0        0
  TXLNB WILD-TYPE         11       25
D272V3, multiclass
            clus
vv           TXLNB MUTATED TXLNB WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               6             127
  STAGE IIA              1              45
  STAGE IIB              4              63
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TXLNB MUTATED     5   9   3   0
  TXLNB WILD-TYPE 150 252  40  18
D272V4, multiclass
    clus
vv   TXLNB MUTATED TXLNB WILD-TYPE
  T1             5             150
  T2             9             252
  T3             3              40
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  TXLNB MUTATED    14   1     2
  TXLNB WILD-TYPE 293  88    70
D272V5, multiclass
       clus
vv      TXLNB MUTATED TXLNB WILD-TYPE
  N0               14             293
  N1                1              88
  N2+N3             2              70
[1] 3 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
  TXLNB MUTATED    16   0
  TXLNB WILD-TYPE 311  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNB MUTATED     16    0
  TXLNB WILD-TYPE  311   23
   clus
vv  TXLNB MUTATED TXLNB WILD-TYPE
  0            16             311
  1             0              23
[1] 2 2
[1] FALSE
D272V7, binary
                 cls
clus                0   1
  TXLNB MUTATED     8   9
  TXLNB WILD-TYPE 251 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNB MUTATED      8    9
  TXLNB WILD-TYPE  251  212
        clus
vv       TXLNB MUTATED TXLNB WILD-TYPE
  FEMALE             8             251
  MALE               9             212
[1] 2 2
[1] FALSE
D272V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TXLNB MUTATED                            1                                 3
  TXLNB WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TXLNB MUTATED                                                   11
  TXLNB WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TXLNB MUTATED                                            0
  TXLNB WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TXLNB MUTATED                                               1
  TXLNB WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TXLNB MUTATED                                0
  TXLNB WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TXLNB MUTATED                                    0
  TXLNB WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TXLNB MUTATED                              0                             0
  TXLNB WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TXLNB MUTATED                                               1
  TXLNB WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TXLNB MUTATED                              0
  TXLNB WILD-TYPE                            9
D272V9, multiclass
                                                    clus
vv                                                   TXLNB MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   TXLNB WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V10, binary
                 cls
clus                0   1
  TXLNB MUTATED     0  17
  TXLNB WILD-TYPE  20 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNB MUTATED      0   17
  TXLNB WILD-TYPE   20  443
     clus
vv    TXLNB MUTATED TXLNB WILD-TYPE
  NO              0              20
  YES            17             443
[1] 2 2
[1] FALSE
D272V11, continuous
D272V12, continuous
                 vv
clus               R0  R1  R2  RX
  TXLNB MUTATED    12   0   0   1
  TXLNB WILD-TYPE 298  11   4  24
D272V13, multiclass
    clus
vv   TXLNB MUTATED TXLNB WILD-TYPE
  R0            12             298
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXLNB MUTATED                                  0     0
  TXLNB WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TXLNB MUTATED                           0    16
  TXLNB WILD-TYPE                        29   361
D272V14, multiclass
                                  clus
vv                                 TXLNB MUTATED TXLNB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       16             361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V15, binary
                 cls
clus                0   1
  TXLNB MUTATED     0  15
  TXLNB WILD-TYPE   6 334
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNB MUTATED      0   15
  TXLNB WILD-TYPE    6  334
                        clus
vv                       TXLNB MUTATED TXLNB WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            15             334
[1] 2 2
[1] FALSE

Clustering(273) Variable = HSPA1L MUTATION ANALYSIS
D273V1, survival
                  sevent
clus2                0   1
  HSPA1L MUTATED     8   1
  HSPA1L WILD-TYPE 307 140
  HSPA1L MUTATED HSPA1L WILD-TYPE 
               9              447 
  HSPA1L MUTATED HSPA1L WILD-TYPE 
               1              140 
$`HSPA1L MUTATED`
TCGA-05-4382 TCGA-05-4430 TCGA-44-A479 TCGA-44-A4SS TCGA-49-4507 TCGA-55-6969 
       19.96        25.02        15.98        13.64         8.81        40.73 
TCGA-55-7994 TCGA-91-6848 TCGA-95-7567 
       19.82         7.36        18.67 

$`HSPA1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU 
        8.55        15.32         9.44        11.08        11.54        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       14.07        32.84        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 
        2.86         0.07        32.65         0.79        42.51        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         1.22         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  HSPA1L MUTATED HSPA1L WILD-TYPE 
            7.36             0.00 
  HSPA1L MUTATED HSPA1L WILD-TYPE 
           40.73           223.96 
  HSPA1L MUTATED HSPA1L WILD-TYPE 
           18.67            17.98 
[1] "7.4 - 40.7 (18.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2"  
D273V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HSPA1L MUTATED         0        1        4         0         3          2
  HSPA1L WILD-TYPE       4      122      129        46        64         68
                  vv
clus               STAGE IIIB STAGE IV
  HSPA1L MUTATED            0        0
  HSPA1L WILD-TYPE         11       25
D273V3, multiclass
            clus
vv           HSPA1L MUTATED HSPA1L WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                4              129
  STAGE IIA               0               46
  STAGE IIB               3               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HSPA1L MUTATED     1   7   2   0
  HSPA1L WILD-TYPE 154 254  41  18
D273V4, multiclass
    clus
vv   HSPA1L MUTATED HSPA1L WILD-TYPE
  T1              1              154
  T2              7              254
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  HSPA1L MUTATED     6   3     1
  HSPA1L WILD-TYPE 301  86    71
D273V5, multiclass
       clus
vv      HSPA1L MUTATED HSPA1L WILD-TYPE
  N0                 6              301
  N1                 3               86
  N2+N3              1               71
[1] 3 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
  HSPA1L MUTATED     7   0
  HSPA1L WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA1L MUTATED      7    0
  HSPA1L WILD-TYPE  320   23
   clus
vv  HSPA1L MUTATED HSPA1L WILD-TYPE
  0              7              320
  1              0               23
[1] 2 2
[1] FALSE
D273V7, binary
                  cls
clus                 0   1
  HSPA1L MUTATED     4   6
  HSPA1L WILD-TYPE 255 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA1L MUTATED      4    6
  HSPA1L WILD-TYPE  255  215
        clus
vv       HSPA1L MUTATED HSPA1L WILD-TYPE
  FEMALE              4              255
  MALE                6              215
[1] 2 2
[1] FALSE
D273V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HSPA1L MUTATED                            0                                 3
  HSPA1L WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HSPA1L MUTATED                                                    7
  HSPA1L WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HSPA1L MUTATED                                            0
  HSPA1L WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HSPA1L MUTATED                                               0
  HSPA1L WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  HSPA1L MUTATED                                0
  HSPA1L WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  HSPA1L MUTATED                                    0
  HSPA1L WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HSPA1L MUTATED                              0                             0
  HSPA1L WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HSPA1L MUTATED                                               0
  HSPA1L WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  HSPA1L MUTATED                              0
  HSPA1L WILD-TYPE                            9
D273V9, multiclass
                                                    clus
vv                                                   HSPA1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   HSPA1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V10, binary
                  cls
clus                 0   1
  HSPA1L MUTATED     1   9
  HSPA1L WILD-TYPE  19 451
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA1L MUTATED      1    9
  HSPA1L WILD-TYPE   19  451
     clus
vv    HSPA1L MUTATED HSPA1L WILD-TYPE
  NO               1               19
  YES              9              451
[1] 2 2
[1] FALSE
D273V11, continuous
D273V12, continuous
                  vv
clus                R0  R1  R2  RX
  HSPA1L MUTATED     6   0   0   0
  HSPA1L WILD-TYPE 304  11   4  25
D273V13, multiclass
    clus
vv   HSPA1L MUTATED HSPA1L WILD-TYPE
  R0              6              304
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSPA1L MUTATED                                  0     0
  HSPA1L WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HSPA1L MUTATED                           1     6
  HSPA1L WILD-TYPE                        28   371
D273V14, multiclass
                                  clus
vv                                 HSPA1L MUTATED HSPA1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         6              371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V15, binary
                  cls
clus                 0   1
  HSPA1L MUTATED     0   6
  HSPA1L WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA1L MUTATED      0    6
  HSPA1L WILD-TYPE    6  343
                        clus
vv                       HSPA1L MUTATED HSPA1L WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              343
[1] 2 2
[1] FALSE

Clustering(274) Variable = NUMA1 MUTATION ANALYSIS
D274V1, survival
                 sevent
clus2               0   1
  NUMA1 MUTATED     8   8
  NUMA1 WILD-TYPE 307 133
  NUMA1 MUTATED NUMA1 WILD-TYPE 
             16             440 
  NUMA1 MUTATED NUMA1 WILD-TYPE 
              8             133 
$`NUMA1 MUTATED`
TCGA-05-4396 TCGA-38-4628 TCGA-44-7667 TCGA-50-6590 TCGA-55-6982 TCGA-55-7724 
        9.96        49.05        36.07        42.35        32.71        23.18 
TCGA-55-7995 TCGA-62-A46S TCGA-62-A471 TCGA-78-7155 TCGA-83-5908 TCGA-91-6830 
        0.16        54.35        40.96        38.50        27.09         1.97 
TCGA-93-A4JN TCGA-95-7567 TCGA-MP-A4T9 TCGA-O1-A52J 
       23.61        18.67        41.59        59.11 

$`NUMA1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       37.71        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       16.44        14.60        19.46        12.03         7.17        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        22.55         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         3.12         1.32         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       56.71        67.96        72.30        13.61        39.25        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55       110.50        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO 
        1.45        19.82         9.76         4.18         6.12         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
       19.00        17.29         1.12         1.22         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.49         5.29        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R 
        0.43        19.82 

  NUMA1 MUTATED NUMA1 WILD-TYPE 
           0.16            0.00 
  NUMA1 MUTATED NUMA1 WILD-TYPE 
          59.11          223.96 
  NUMA1 MUTATED NUMA1 WILD-TYPE 
         34.390          17.635 
[1] "0.2 - 59.1 (34.4)"  "0.0 - 224.0 (17.6)"
[1] "hr=" "1.1"
D274V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NUMA1 MUTATED         0        3        4         1         6          1
  NUMA1 WILD-TYPE       4      120      129        45        61         69
                 vv
clus              STAGE IIIB STAGE IV
  NUMA1 MUTATED            1        1
  NUMA1 WILD-TYPE         10       24
D274V3, multiclass
            clus
vv           NUMA1 MUTATED NUMA1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              6              61
  STAGE IIIA             1              69
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUMA1 MUTATED     4  11   1   1
  NUMA1 WILD-TYPE 151 250  42  17
D274V4, multiclass
    clus
vv   NUMA1 MUTATED NUMA1 WILD-TYPE
  T1             4             151
  T2            11             250
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  NUMA1 MUTATED     9   7     1
  NUMA1 WILD-TYPE 298  82    71
D274V5, multiclass
       clus
vv      NUMA1 MUTATED NUMA1 WILD-TYPE
  N0                9             298
  N1                7              82
  N2+N3             1              71
[1] 3 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
  NUMA1 MUTATED    11   1
  NUMA1 WILD-TYPE 316  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMA1 MUTATED     11    1
  NUMA1 WILD-TYPE  316   22
   clus
vv  NUMA1 MUTATED NUMA1 WILD-TYPE
  0            11             316
  1             1              22
[1] 2 2
[1] FALSE
D274V7, binary
                 cls
clus                0   1
  NUMA1 MUTATED    11   6
  NUMA1 WILD-TYPE 248 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMA1 MUTATED     11    6
  NUMA1 WILD-TYPE  248  215
        clus
vv       NUMA1 MUTATED NUMA1 WILD-TYPE
  FEMALE            11             248
  MALE               6             215
[1] 2 2
[1] FALSE
D274V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NUMA1 MUTATED                            1                                 2
  NUMA1 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NUMA1 MUTATED                                                   13
  NUMA1 WILD-TYPE                                                281
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NUMA1 MUTATED                                            0
  NUMA1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NUMA1 MUTATED                                               0
  NUMA1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NUMA1 MUTATED                                0
  NUMA1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NUMA1 MUTATED                                    0
  NUMA1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NUMA1 MUTATED                              0                             1
  NUMA1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NUMA1 MUTATED                                               0
  NUMA1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NUMA1 MUTATED                              0
  NUMA1 WILD-TYPE                            9
D274V9, multiclass
                                                    clus
vv                                                   NUMA1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NUMA1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V10, binary
                 cls
clus                0   1
  NUMA1 MUTATED     0  17
  NUMA1 WILD-TYPE  20 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMA1 MUTATED      0   17
  NUMA1 WILD-TYPE   20  443
     clus
vv    NUMA1 MUTATED NUMA1 WILD-TYPE
  NO              0              20
  YES            17             443
[1] 2 2
[1] FALSE
D274V11, continuous
D274V12, continuous
                 vv
clus               R0  R1  R2  RX
  NUMA1 MUTATED     9   0   0   2
  NUMA1 WILD-TYPE 301  11   4  23
D274V13, multiclass
    clus
vv   NUMA1 MUTATED NUMA1 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUMA1 MUTATED                                  0     0
  NUMA1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NUMA1 MUTATED                           0    15
  NUMA1 WILD-TYPE                        29   362
D274V14, multiclass
                                  clus
vv                                 NUMA1 MUTATED NUMA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       15             362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V15, binary
                 cls
clus                0   1
  NUMA1 MUTATED     0  13
  NUMA1 WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMA1 MUTATED      0   13
  NUMA1 WILD-TYPE    6  336
                        clus
vv                       NUMA1 MUTATED NUMA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(275) Variable = MEFV MUTATION ANALYSIS
D275V1, survival
                sevent
clus2              0   1
  MEFV MUTATED    13   4
  MEFV WILD-TYPE 302 137
  MEFV MUTATED MEFV WILD-TYPE 
            17            439 
  MEFV MUTATED MEFV WILD-TYPE 
             4            137 
$`MEFV MUTATED`
TCGA-38-4629 TCGA-44-6144 TCGA-44-A479 TCGA-44-A47F TCGA-49-6744 TCGA-55-7570 
       28.41        23.77        15.98        11.08        29.26         0.20 
TCGA-55-7907 TCGA-55-8506 TCGA-62-A46O TCGA-67-3771 TCGA-69-7765 TCGA-69-7978 
        0.53         0.36        47.80        20.05         5.42         2.30 
TCGA-78-7146 TCGA-78-7220 TCGA-86-8358 TCGA-J2-8194 TCGA-MN-A4N5 
        5.69        26.53        21.47        23.80         2.76 

$`MEFV WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
      120.79        37.71        49.05        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        28.37        12.59        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       14.63        12.13        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 
        1.12         0.79         1.78         1.45        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       13.61         7.56         6.05         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
        7.07       104.19       223.96         8.48        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81         0.20        27.19        38.63        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  MEFV MUTATED MEFV WILD-TYPE 
           0.2            0.0 
  MEFV MUTATED MEFV WILD-TYPE 
         47.80         223.96 
  MEFV MUTATED MEFV WILD-TYPE 
         15.98          18.08 
[1] "0.2 - 47.8 (16.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D275V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MEFV MUTATED         0        4        3         2         5          2
  MEFV WILD-TYPE       4      119      130        44        62         68
                vv
clus             STAGE IIIB STAGE IV
  MEFV MUTATED            0        1
  MEFV WILD-TYPE         11       24
D275V3, multiclass
            clus
vv           MEFV MUTATED MEFV WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              3            130
  STAGE IIA             2             44
  STAGE IIB             5             62
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MEFV MUTATED     4   9   3   1
  MEFV WILD-TYPE 151 252  40  17
D275V4, multiclass
    clus
vv   MEFV MUTATED MEFV WILD-TYPE
  T1            4            151
  T2            9            252
  T3            3             40
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  MEFV MUTATED    11   4     2
  MEFV WILD-TYPE 296  85    70
D275V5, multiclass
       clus
vv      MEFV MUTATED MEFV WILD-TYPE
  N0              11            296
  N1               4             85
  N2+N3            2             70
[1] 3 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
  MEFV MUTATED     9   0
  MEFV WILD-TYPE 318  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEFV MUTATED      9    0
  MEFV WILD-TYPE  318   23
   clus
vv  MEFV MUTATED MEFV WILD-TYPE
  0            9            318
  1            0             23
[1] 2 2
[1] FALSE
D275V7, binary
                cls
clus               0   1
  MEFV MUTATED     8   9
  MEFV WILD-TYPE 251 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEFV MUTATED      8    9
  MEFV WILD-TYPE  251  212
        clus
vv       MEFV MUTATED MEFV WILD-TYPE
  FEMALE            8            251
  MALE              9            212
[1] 2 2
[1] FALSE
D275V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MEFV MUTATED                            0                                 6
  MEFV WILD-TYPE                         18                                96
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MEFV MUTATED                                                   11
  MEFV WILD-TYPE                                                283
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MEFV MUTATED                                            0
  MEFV WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MEFV MUTATED                                               0
  MEFV WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MEFV MUTATED                                0
  MEFV WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MEFV MUTATED                                    0
  MEFV WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MEFV MUTATED                              0                             0
  MEFV WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MEFV MUTATED                                               0
  MEFV WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MEFV MUTATED                              0
  MEFV WILD-TYPE                            9
D275V9, multiclass
                                                    clus
vv                                                   MEFV MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MEFV WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V10, binary
                cls
clus               0   1
  MEFV MUTATED     1  16
  MEFV WILD-TYPE  19 444
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEFV MUTATED      1   16
  MEFV WILD-TYPE   19  444
     clus
vv    MEFV MUTATED MEFV WILD-TYPE
  NO             1             19
  YES           16            444
[1] 2 2
[1] FALSE
D275V11, continuous
D275V12, continuous
                vv
clus              R0  R1  R2  RX
  MEFV MUTATED    12   0   0   1
  MEFV WILD-TYPE 298  11   4  24
D275V13, multiclass
    clus
vv   MEFV MUTATED MEFV WILD-TYPE
  R0           12            298
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MEFV MUTATED                                  0     0
  MEFV WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MEFV MUTATED                           4    13
  MEFV WILD-TYPE                        25   364
D275V14, multiclass
                                  clus
vv                                 MEFV MUTATED MEFV WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   4             25
  WHITE                                      13            364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V15, binary
                cls
clus               0   1
  MEFV MUTATED     0  14
  MEFV WILD-TYPE   6 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEFV MUTATED      0   14
  MEFV WILD-TYPE    6  335
                        clus
vv                       MEFV MUTATED MEFV WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           14            335
[1] 2 2
[1] FALSE

Clustering(276) Variable = GAN MUTATION ANALYSIS
D276V1, survival
               sevent
clus2             0   1
  GAN MUTATED     4   6
  GAN WILD-TYPE 311 135
  GAN MUTATED GAN WILD-TYPE 
           10           446 
  GAN MUTATED GAN WILD-TYPE 
            6           135 
$`GAN MUTATED`
TCGA-05-4249 TCGA-05-4396 TCGA-44-3918 TCGA-49-4494 TCGA-53-7626 TCGA-55-7574 
       50.07         9.96        34.06        35.54        30.54         3.12 
TCGA-62-A46O TCGA-78-7150 TCGA-91-6830 TCGA-MP-A4TK 
       47.80        21.90         1.97        19.13 

$`GAN WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 
       13.45        76.21        28.11        28.57        12.66        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        34.29        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58        35.93        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62        41.36        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        14.66        14.10        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  GAN MUTATED GAN WILD-TYPE 
         1.97          0.00 
  GAN MUTATED GAN WILD-TYPE 
        50.07        223.96 
  GAN MUTATED GAN WILD-TYPE 
       26.220        17.835 
[1] "2.0 - 50.1 (26.2)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.7"
D276V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GAN MUTATED         0        1        3         2         2          1
  GAN WILD-TYPE       4      122      130        44        65         69
               vv
clus            STAGE IIIB STAGE IV
  GAN MUTATED            1        0
  GAN WILD-TYPE         10       25
D276V3, multiclass
            clus
vv           GAN MUTATED GAN WILD-TYPE
  STAGE I              0             4
  STAGE IA             1           122
  STAGE IB             3           130
  STAGE IIA            2            44
  STAGE IIB            2            65
  STAGE IIIA           1            69
  STAGE IIIB           1            10
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  GAN MUTATED     3   5   1   1
  GAN WILD-TYPE 152 256  42  17
D276V4, multiclass
    clus
vv   GAN MUTATED GAN WILD-TYPE
  T1           3           152
  T2           5           256
  T3           1            42
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  GAN MUTATED     4   5     1
  GAN WILD-TYPE 303  84    71
D276V5, multiclass
       clus
vv      GAN MUTATED GAN WILD-TYPE
  N0              4           303
  N1              5            84
  N2+N3           1            71
[1] 3 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
  GAN MUTATED     8   0
  GAN WILD-TYPE 319  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      8    0
  GAN WILD-TYPE  319   23
   clus
vv  GAN MUTATED GAN WILD-TYPE
  0           8           319
  1           0            23
[1] 2 2
[1] FALSE
D276V7, binary
               cls
clus              0   1
  GAN MUTATED     6   4
  GAN WILD-TYPE 253 217
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      6    4
  GAN WILD-TYPE  253  217
        clus
vv       GAN MUTATED GAN WILD-TYPE
  FEMALE           6           253
  MALE             4           217
[1] 2 2
[1] FALSE
D276V8, continuous
[1] "Remove cluster labels:" "GAN MUTATED"           
clus
  GAN MUTATED GAN WILD-TYPE 
            1            83 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46P    TCGA-62-A46R 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y    TCGA-62-A470 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681    TCGA-64-5778 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520    TCGA-73-4659 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-86-8279    TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-86-8669    TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
   TCGA-MN-A4N1    TCGA-MN-A4N4    TCGA-MN-A4N5 
"GAN WILD-TYPE" "GAN WILD-TYPE" "GAN WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GAN MUTATED                            0                                 1
  GAN WILD-TYPE                         18                               101
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GAN MUTATED                                                    9
  GAN WILD-TYPE                                                285
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GAN MUTATED                                            0
  GAN WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GAN MUTATED                                               0
  GAN WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  GAN MUTATED                                0
  GAN WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  GAN MUTATED                                    0                            0
  GAN WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  GAN MUTATED                               0
  GAN WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GAN MUTATED                                               0
  GAN WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  GAN MUTATED                              0
  GAN WILD-TYPE                            9
D276V9, multiclass
                                                    clus
vv                                                   GAN MUTATED GAN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            1           101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           9           285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V10, binary
               cls
clus              0   1
  GAN MUTATED     1   9
  GAN WILD-TYPE  19 451
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      1    9
  GAN WILD-TYPE   19  451
     clus
vv    GAN MUTATED GAN WILD-TYPE
  NO            1            19
  YES           9           451
[1] 2 2
[1] FALSE
D276V11, continuous
D276V12, continuous
               vv
clus             R0  R1  R2  RX
  GAN MUTATED     8   1   0   0
  GAN WILD-TYPE 302  10   4  25
D276V13, multiclass
    clus
vv   GAN MUTATED GAN WILD-TYPE
  R0           8           302
  R1           1            10
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAN MUTATED                                  0     0
  GAN WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GAN MUTATED                           0     7
  GAN WILD-TYPE                        29   370
D276V14, multiclass
                                  clus
vv                                 GAN MUTATED GAN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                      7           370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V15, binary
               cls
clus              0   1
  GAN MUTATED     0   6
  GAN WILD-TYPE   6 343
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      0    6
  GAN WILD-TYPE    6  343
                        clus
vv                       GAN MUTATED GAN WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           6           343
[1] 2 2
[1] FALSE

Clustering(277) Variable = SQSTM1 MUTATION ANALYSIS
D277V1, survival
                  sevent
clus2                0   1
  SQSTM1 MUTATED     5   1
  SQSTM1 WILD-TYPE 310 140
  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
               6              450 
  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
               1              140 
$`SQSTM1 MUTATED`
TCGA-05-4384 TCGA-44-2656 TCGA-50-5072 TCGA-53-7813 TCGA-62-A471 TCGA-MN-A4N4 
       14.01        46.98         8.22        13.94        40.96        38.63 

$`SQSTM1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        34.29        30.54         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       72.30        13.61        39.25        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
            8.22             0.00 
  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
           46.98           223.96 
  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
           26.32            18.03 
[1] "8.2 - 47.0 (26.3)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.3"
D277V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SQSTM1 MUTATED         0        1        1         0         1          2
  SQSTM1 WILD-TYPE       4      122      132        46        66         68
                  vv
clus               STAGE IIIB STAGE IV
  SQSTM1 MUTATED            1        0
  SQSTM1 WILD-TYPE         10       25
D277V3, multiclass
            clus
vv           SQSTM1 MUTATED SQSTM1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                1              132
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SQSTM1 MUTATED     1   4   0   1
  SQSTM1 WILD-TYPE 154 257  43  17
D277V4, multiclass
    clus
vv   SQSTM1 MUTATED SQSTM1 WILD-TYPE
  T1              1              154
  T2              4              257
  T3              0               43
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  SQSTM1 MUTATED     3   1     2
  SQSTM1 WILD-TYPE 304  88    70
D277V5, multiclass
       clus
vv      SQSTM1 MUTATED SQSTM1 WILD-TYPE
  N0                 3              304
  N1                 1               88
  N2+N3              2               70
[1] 3 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
  SQSTM1 MUTATED     6   0
  SQSTM1 WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SQSTM1 MUTATED      6    0
  SQSTM1 WILD-TYPE  321   23
   clus
vv  SQSTM1 MUTATED SQSTM1 WILD-TYPE
  0              6              321
  1              0               23
[1] 2 2
[1] FALSE
D277V7, binary
                  cls
clus                 0   1
  SQSTM1 MUTATED     1   5
  SQSTM1 WILD-TYPE 258 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SQSTM1 MUTATED      1    5
  SQSTM1 WILD-TYPE  258  216
        clus
vv       SQSTM1 MUTATED SQSTM1 WILD-TYPE
  FEMALE              1              258
  MALE                5              216
[1] 2 2
[1] FALSE
D277V8, continuous
[1] "Remove cluster labels:" "SQSTM1 MUTATED"        
clus
  SQSTM1 MUTATED SQSTM1 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N5 
"SQSTM1 WILD-TYPE" "SQSTM1 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SQSTM1 MUTATED                            0                                 1
  SQSTM1 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SQSTM1 MUTATED                                                    4
  SQSTM1 WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SQSTM1 MUTATED                                            0
  SQSTM1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SQSTM1 MUTATED                                               1
  SQSTM1 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SQSTM1 MUTATED                                0
  SQSTM1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SQSTM1 MUTATED                                    0
  SQSTM1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SQSTM1 MUTATED                              0                             0
  SQSTM1 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SQSTM1 MUTATED                                               0
  SQSTM1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SQSTM1 MUTATED                              0
  SQSTM1 WILD-TYPE                            9
D277V9, multiclass
                                                    clus
vv                                                   SQSTM1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SQSTM1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V10, binary
                  cls
clus                 0   1
  SQSTM1 MUTATED     1   5
  SQSTM1 WILD-TYPE  19 455
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SQSTM1 MUTATED      1    5
  SQSTM1 WILD-TYPE   19  455
     clus
vv    SQSTM1 MUTATED SQSTM1 WILD-TYPE
  NO               1               19
  YES              5              455
[1] 2 2
[1] FALSE
D277V11, continuous
D277V12, continuous
                  vv
clus                R0  R1  R2  RX
  SQSTM1 MUTATED     2   0   0   1
  SQSTM1 WILD-TYPE 308  11   4  24
D277V13, multiclass
    clus
vv   SQSTM1 MUTATED SQSTM1 WILD-TYPE
  R0              2              308
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SQSTM1 MUTATED                                  0     0
  SQSTM1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SQSTM1 MUTATED                           0     5
  SQSTM1 WILD-TYPE                        29   372
D277V14, multiclass
                                  clus
vv                                 SQSTM1 MUTATED SQSTM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V15, binary
                  cls
clus                 0   1
  SQSTM1 MUTATED     0   5
  SQSTM1 WILD-TYPE   6 344
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SQSTM1 MUTATED      0    5
  SQSTM1 WILD-TYPE    6  344
                        clus
vv                       SQSTM1 MUTATED SQSTM1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              344
[1] 2 2
[1] FALSE

Clustering(278) Variable = DSN1 MUTATION ANALYSIS
D278V1, survival
                sevent
clus2              0   1
  DSN1 MUTATED     3   3
  DSN1 WILD-TYPE 312 138
  DSN1 MUTATED DSN1 WILD-TYPE 
             6            450 
  DSN1 MUTATED DSN1 WILD-TYPE 
             3            138 
$`DSN1 MUTATED`
TCGA-38-4631 TCGA-50-5939 TCGA-69-7980 TCGA-73-4659 TCGA-93-8067 TCGA-95-7043 
       11.64        15.12        12.56        23.38         6.12         1.22 

$`DSN1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 
       14.27        40.60        78.67        21.47         8.45        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30         2.93        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01         0.10        52.60        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.12         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  DSN1 MUTATED DSN1 WILD-TYPE 
          1.22           0.00 
  DSN1 MUTATED DSN1 WILD-TYPE 
         23.38         223.96 
  DSN1 MUTATED DSN1 WILD-TYPE 
         12.10          18.15 
[1] "1.2 - 23.4 (12.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "4.1"
D278V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DSN1 MUTATED         1        1        3         0         0          1
  DSN1 WILD-TYPE       3      122      130        46        67         69
                vv
clus             STAGE IIIB STAGE IV
  DSN1 MUTATED            0        0
  DSN1 WILD-TYPE         11       25
D278V3, multiclass
            clus
vv           DSN1 MUTATED DSN1 WILD-TYPE
  STAGE I               1              3
  STAGE IA              1            122
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSN1 MUTATED     2   4   0   0
  DSN1 WILD-TYPE 153 257  43  18
D278V4, multiclass
    clus
vv   DSN1 MUTATED DSN1 WILD-TYPE
  T1            2            153
  T2            4            257
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  DSN1 MUTATED     5   0     1
  DSN1 WILD-TYPE 302  89    71
D278V5, multiclass
       clus
vv      DSN1 MUTATED DSN1 WILD-TYPE
  N0               5            302
  N1               0             89
  N2+N3            1             71
[1] 3 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
  DSN1 MUTATED     4   0
  DSN1 WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSN1 MUTATED      4    0
  DSN1 WILD-TYPE  323   23
   clus
vv  DSN1 MUTATED DSN1 WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D278V7, binary
                cls
clus               0   1
  DSN1 MUTATED     3   3
  DSN1 WILD-TYPE 256 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSN1 MUTATED      3    3
  DSN1 WILD-TYPE  256  218
        clus
vv       DSN1 MUTATED DSN1 WILD-TYPE
  FEMALE            3            256
  MALE              3            218
[1] 2 2
[1] FALSE
D278V8, continuous
[1] "Remove cluster labels:" "DSN1 MUTATED"          
clus
  DSN1 MUTATED DSN1 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"DSN1 WILD-TYPE" "DSN1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DSN1 MUTATED                            0                                 2
  DSN1 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DSN1 MUTATED                                                    4
  DSN1 WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DSN1 MUTATED                                            0
  DSN1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DSN1 MUTATED                                               0
  DSN1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  DSN1 MUTATED                                0
  DSN1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  DSN1 MUTATED                                    0
  DSN1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DSN1 MUTATED                              0                             0
  DSN1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DSN1 MUTATED                                               0
  DSN1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  DSN1 MUTATED                              0
  DSN1 WILD-TYPE                            9
D278V9, multiclass
                                                    clus
vv                                                   DSN1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   DSN1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V10, binary
                cls
clus               0   1
  DSN1 MUTATED     0   6
  DSN1 WILD-TYPE  20 454
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSN1 MUTATED      0    6
  DSN1 WILD-TYPE   20  454
     clus
vv    DSN1 MUTATED DSN1 WILD-TYPE
  NO             0             20
  YES            6            454
[1] 2 2
[1] FALSE
D278V11, continuous
D278V12, continuous
                vv
clus              R0  R1  R2  RX
  DSN1 MUTATED     2   0   0   1
  DSN1 WILD-TYPE 308  11   4  24
D278V13, multiclass
    clus
vv   DSN1 MUTATED DSN1 WILD-TYPE
  R0            2            308
  R1            0             11
  R2            0              4
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSN1 MUTATED                                  0     1
  DSN1 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSN1 MUTATED                           0     5
  DSN1 WILD-TYPE                        29   372
D278V14, multiclass
                                  clus
vv                                 DSN1 MUTATED DSN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V15, binary
                cls
clus               0   1
  DSN1 MUTATED     0   6
  DSN1 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSN1 MUTATED      0    6
  DSN1 WILD-TYPE    6  343
                        clus
vv                       DSN1 MUTATED DSN1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(279) Variable = NAAA MUTATION ANALYSIS
D279V1, survival
                sevent
clus2              0   1
  NAAA MUTATED     2   1
  NAAA WILD-TYPE 313 140
  NAAA MUTATED NAAA WILD-TYPE 
             3            453 
  NAAA MUTATED NAAA WILD-TYPE 
             1            140 
$`NAAA MUTATED`
TCGA-38-4632 TCGA-55-7816 TCGA-91-7771 
       44.61         1.45        16.18 

$`NAAA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  NAAA MUTATED NAAA WILD-TYPE 
          1.45           0.00 
  NAAA MUTATED NAAA WILD-TYPE 
         44.61         223.96 
  NAAA MUTATED NAAA WILD-TYPE 
         16.18          18.08 
[1] "1.4 - 44.6 (16.2)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D279V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NAAA MUTATED         0        0        0         0         1          0
  NAAA WILD-TYPE       4      123      133        46        66         70
                vv
clus             STAGE IIIB STAGE IV
  NAAA MUTATED            0        2
  NAAA WILD-TYPE         11       23
D279V3, multiclass
            clus
vv           NAAA MUTATED NAAA WILD-TYPE
  STAGE I               0              4
  STAGE IA              0            123
  STAGE IB              0            133
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NAAA MUTATED     0   1   1   0
  NAAA WILD-TYPE 155 260  42  18
D279V4, multiclass
[1] "Remove cluster labels:" "NAAA MUTATED"          
clus
  NAAA MUTATED NAAA WILD-TYPE 
             2            475 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-4123 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-4627 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-4628     TCGA-38-4629     TCGA-38-4630     TCGA-38-4631 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F     TCGA-44-2656 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-2657     TCGA-44-2661     TCGA-44-2665     TCGA-44-3396 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-3919     TCGA-44-4112 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-5643     TCGA-44-5644     TCGA-44-5645     TCGA-44-6144 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6148 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7671     TCGA-44-7672     TCGA-44-8117 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4487     TCGA-49-4488 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4490     TCGA-49-4494     TCGA-49-4501     TCGA-49-4505 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4507     TCGA-49-4510     TCGA-49-4512 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4514     TCGA-49-6742     TCGA-49-6743     TCGA-49-6744 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-6745     TCGA-49-6761     TCGA-49-6767     TCGA-50-5044 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5045     TCGA-50-5049     TCGA-50-5051     TCGA-50-5055 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5066     TCGA-50-5068     TCGA-50-5072     TCGA-50-5930 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5932     TCGA-50-5933     TCGA-50-5935 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5936     TCGA-50-5939     TCGA-50-5941     TCGA-50-5942 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5944     TCGA-50-5946     TCGA-50-6590     TCGA-50-6591 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-6592     TCGA-50-6593     TCGA-50-6594     TCGA-50-6595 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-6597     TCGA-50-6673     TCGA-50-7109     TCGA-50-8457 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-8459     TCGA-50-8460     TCGA-53-7624     TCGA-53-7626 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-1592     TCGA-55-1595 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-5899     TCGA-55-6543     TCGA-55-6642     TCGA-55-6712 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6968     TCGA-55-6969     TCGA-55-6970     TCGA-55-6971 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6972     TCGA-55-6975     TCGA-55-6978     TCGA-55-6979 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6980     TCGA-55-6981     TCGA-55-6982     TCGA-55-6983 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6984     TCGA-55-6985     TCGA-55-6986     TCGA-55-6987 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7227     TCGA-55-7281     TCGA-55-7283     TCGA-55-7284 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7573     TCGA-55-7574     TCGA-55-7576 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7724     TCGA-55-7725     TCGA-55-7726     TCGA-55-7727 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7728     TCGA-55-7815     TCGA-55-7903     TCGA-55-7907 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7914     TCGA-55-7994 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7995     TCGA-55-8085     TCGA-55-8087     TCGA-55-8089 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8090     TCGA-55-8091     TCGA-55-8092     TCGA-55-8094 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8096     TCGA-55-8097     TCGA-55-8203     TCGA-55-8204 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8206     TCGA-55-8207     TCGA-55-8208 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8505 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8508     TCGA-55-8510 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8513     TCGA-55-8514 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8614     TCGA-55-8615     TCGA-55-8616     TCGA-55-8619 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-1676     TCGA-64-1677     TCGA-64-1679     TCGA-64-1681 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-5781     TCGA-64-5815     TCGA-67-3771     TCGA-67-3772 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-67-3773     TCGA-67-4679     TCGA-67-6215     TCGA-67-6216 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-67-6217     TCGA-69-7760     TCGA-69-7761     TCGA-69-7763 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-7764     TCGA-69-7765     TCGA-69-7973     TCGA-69-7974 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-7978     TCGA-69-7979     TCGA-69-7980     TCGA-69-8253 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-8254     TCGA-69-8255     TCGA-69-A59K     TCGA-71-6725 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4658     TCGA-73-4659     TCGA-73-4662 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4666     TCGA-73-4668     TCGA-73-4670     TCGA-73-4675 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4676     TCGA-73-4677     TCGA-73-7498     TCGA-73-7499 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-5122     TCGA-75-5125     TCGA-75-5126     TCGA-75-5146 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-5147     TCGA-75-6203     TCGA-75-6205     TCGA-75-6206 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-6207     TCGA-75-6211     TCGA-75-6212     TCGA-75-6214 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-7025     TCGA-75-7027     TCGA-75-7030     TCGA-75-7031 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7143     TCGA-78-7145     TCGA-78-7146     TCGA-78-7147 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7148     TCGA-78-7149     TCGA-78-7150     TCGA-78-7152 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7153     TCGA-78-7154     TCGA-78-7155     TCGA-78-7156 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7158     TCGA-78-7159     TCGA-78-7160     TCGA-78-7161 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7162     TCGA-78-7163     TCGA-78-7166     TCGA-78-7167 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7540     TCGA-78-7542     TCGA-78-7633 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-8640     TCGA-78-8648     TCGA-78-8655     TCGA-78-8660 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-8662     TCGA-80-5607     TCGA-80-5608     TCGA-80-5611 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6562     TCGA-86-6851     TCGA-86-7701 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-7711     TCGA-86-7713     TCGA-86-7714     TCGA-86-7953 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8054     TCGA-86-8055 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8281     TCGA-86-8358     TCGA-86-8359     TCGA-86-8585 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-8672 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8673     TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-A4P7     TCGA-86-A4P8     TCGA-91-6828     TCGA-91-6829 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-6830     TCGA-91-6831     TCGA-91-6835     TCGA-91-6836 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6847     TCGA-91-6848     TCGA-91-6849 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-8496     TCGA-91-8497     TCGA-91-8499     TCGA-91-A4BC 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7039 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-7043     TCGA-95-7562     TCGA-95-7567     TCGA-95-7944 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-7947     TCGA-95-7948     TCGA-95-8039     TCGA-95-8494 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-7547     TCGA-97-7552     TCGA-97-7553     TCGA-97-7554 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-7937     TCGA-97-7938     TCGA-97-7941     TCGA-97-8171 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8175     TCGA-97-8176 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-8177     TCGA-97-8179     TCGA-97-8547     TCGA-97-8552 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M6     TCGA-97-A4M7 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-99-7458     TCGA-99-8025     TCGA-99-8028     TCGA-99-8032 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-J2-8192     TCGA-J2-8194     TCGA-J2-A4AD     TCGA-J2-A4AE 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6     TCGA-L9-A443 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY     TCGA-MP-A4T2 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7     TCGA-MP-A4T8 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TD 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YF     TCGA-NJ-A4YG 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-NJ-A4YI     TCGA-NJ-A4YP     TCGA-NJ-A4YQ     TCGA-NJ-A55A 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-NJ-A55O     TCGA-NJ-A55R     TCGA-O1-A52J 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
                vv
clus              N0  N1 N2+N3
  NAAA MUTATED     1   1     0
  NAAA WILD-TYPE 306  88    72
D279V5, multiclass
[1] "Remove cluster labels:" "NAAA MUTATED"          
clus
  NAAA MUTATED NAAA WILD-TYPE 
             2            466 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4403 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4415     TCGA-05-4417 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4418     TCGA-05-4420     TCGA-05-4422     TCGA-05-4424 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4425     TCGA-05-4426     TCGA-05-4427     TCGA-05-4430 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4432     TCGA-05-4433     TCGA-05-4434     TCGA-05-5420 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-5423     TCGA-05-5425     TCGA-05-5428     TCGA-05-5429 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-5715     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-4627     TCGA-38-4628 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-4629     TCGA-38-4630     TCGA-38-4631     TCGA-38-6178 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-7271     TCGA-38-A44F     TCGA-44-2656     TCGA-44-2661 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-2665     TCGA-44-3396     TCGA-44-3398     TCGA-44-3918 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-3919     TCGA-44-4112     TCGA-44-5643     TCGA-44-5644 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6146     TCGA-44-6148 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6778 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6779     TCGA-44-7659     TCGA-44-7660     TCGA-44-7661 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-7662     TCGA-44-7667     TCGA-44-7669     TCGA-44-7670 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-7671     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4490 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4501     TCGA-49-4505     TCGA-49-4506 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4507     TCGA-49-4510     TCGA-49-4512     TCGA-49-4514 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-49-6745 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-6761     TCGA-49-6767     TCGA-50-5044     TCGA-50-5045 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5049     TCGA-50-5051     TCGA-50-5055     TCGA-50-5066 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5068     TCGA-50-5072     TCGA-50-5930     TCGA-50-5931 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5932     TCGA-50-5933     TCGA-50-5935     TCGA-50-5936 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5939     TCGA-50-5941     TCGA-50-5942     TCGA-50-5944 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5946     TCGA-50-6590     TCGA-50-6591     TCGA-50-6592 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-6593     TCGA-50-6594     TCGA-50-6595     TCGA-50-6597 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-6673     TCGA-50-7109     TCGA-50-8457     TCGA-50-8459 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-8460     TCGA-53-7624     TCGA-53-7626     TCGA-53-7813 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-53-A4EZ     TCGA-55-1592     TCGA-55-1595     TCGA-55-5899 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6543     TCGA-55-6642     TCGA-55-6712     TCGA-55-6968 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6969     TCGA-55-6970     TCGA-55-6971     TCGA-55-6972 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6975     TCGA-55-6978     TCGA-55-6979     TCGA-55-6980 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6981     TCGA-55-6982     TCGA-55-6983     TCGA-55-6984 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6985     TCGA-55-6986     TCGA-55-6987     TCGA-55-7227 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7281     TCGA-55-7283     TCGA-55-7284     TCGA-55-7570 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7573     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7727     TCGA-55-7728 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7815     TCGA-55-7903     TCGA-55-7907     TCGA-55-7910 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7914     TCGA-55-7994     TCGA-55-7995 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8085     TCGA-55-8087     TCGA-55-8089     TCGA-55-8090 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8091     TCGA-55-8092     TCGA-55-8094     TCGA-55-8096 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8097     TCGA-55-8203     TCGA-55-8204     TCGA-55-8205 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8206     TCGA-55-8207     TCGA-55-8208     TCGA-55-8299 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8301     TCGA-55-8302     TCGA-55-8505     TCGA-55-8506 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8510     TCGA-55-8511 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8513     TCGA-55-8514     TCGA-55-8614 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8616     TCGA-55-8619     TCGA-55-8620 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A491     TCGA-55-A492     TCGA-55-A493 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG     TCGA-62-8394 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-8395     TCGA-62-8397     TCGA-62-8398     TCGA-62-8399 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A470     TCGA-62-A471     TCGA-62-A472     TCGA-64-1676 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1679     TCGA-64-1681     TCGA-64-5774 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-5815     TCGA-67-3771     TCGA-67-3772     TCGA-67-3773 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-67-4679     TCGA-67-6215     TCGA-67-6216     TCGA-67-6217 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-7760     TCGA-69-7761     TCGA-69-7763     TCGA-69-7764 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-7765     TCGA-69-7973     TCGA-69-7974     TCGA-69-7978 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-7979     TCGA-69-7980     TCGA-69-8253     TCGA-69-8255 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-A59K     TCGA-71-6725     TCGA-71-8520     TCGA-73-4658 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-4677 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-75-5125 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-5126     TCGA-75-5146     TCGA-75-5147     TCGA-75-6203 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-6205     TCGA-75-6206     TCGA-75-6207     TCGA-75-6211 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-6212     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-7030     TCGA-75-7031     TCGA-78-7143     TCGA-78-7145 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7160 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7166 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7167     TCGA-78-7220     TCGA-78-7535     TCGA-78-7536 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7537     TCGA-78-7539     TCGA-78-7540     TCGA-78-7542 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-80-5611     TCGA-83-5908     TCGA-86-6562     TCGA-86-6851 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-7953     TCGA-86-7954     TCGA-86-7955     TCGA-86-8054 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8073     TCGA-86-8074 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8075     TCGA-86-8076     TCGA-86-8278     TCGA-86-8279 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8280     TCGA-86-8358     TCGA-86-8359     TCGA-86-8585 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-8672 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8673     TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-A4P7     TCGA-86-A4P8     TCGA-91-6828     TCGA-91-6829 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-6830     TCGA-91-6831     TCGA-91-6835     TCGA-91-6836 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6847     TCGA-91-6848     TCGA-91-6849 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-8497     TCGA-91-8499     TCGA-91-A4BC     TCGA-91-A4BD 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7039     TCGA-95-7043 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7567     TCGA-95-7944     TCGA-95-7947 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-7948     TCGA-95-8039     TCGA-95-8494     TCGA-95-A4VK 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546     TCGA-97-7547 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-7552     TCGA-97-7553     TCGA-97-7554     TCGA-97-7937 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-7938     TCGA-97-7941     TCGA-97-8171     TCGA-97-8172 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-8174     TCGA-97-8175     TCGA-97-8176     TCGA-97-8177 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-8179     TCGA-97-8547     TCGA-97-8552     TCGA-97-A4LX 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2     TCGA-97-A4M3 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-A4M5     TCGA-97-A4M6     TCGA-97-A4M7     TCGA-99-7458 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8192 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-J2-8194     TCGA-J2-A4AD     TCGA-J2-A4AE     TCGA-J2-A4AG 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-L4-A4E5     TCGA-L4-A4E6     TCGA-L9-A443     TCGA-L9-A444 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5     TCGA-MP-A4SV 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4SW     TCGA-MP-A4SY     TCGA-MP-A4T2     TCGA-MP-A4T4 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4T6     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TD     TCGA-MP-A4TE 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A5C7     TCGA-NJ-A4YF     TCGA-NJ-A4YG     TCGA-NJ-A4YI 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-NJ-A4YP     TCGA-NJ-A4YQ     TCGA-NJ-A55A     TCGA-NJ-A55O 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-NJ-A55R     TCGA-O1-A52J 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" 
D279V6, binary
                cls
clus               0   1
  NAAA MUTATED     0   1
  NAAA WILD-TYPE 327  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAAA MUTATED      0    1
  NAAA WILD-TYPE  327   22
   clus
vv  NAAA MUTATED NAAA WILD-TYPE
  0            0            327
  1            1             22
[1] 2 2
[1] FALSE
D279V7, binary
                cls
clus               0   1
  NAAA MUTATED     1   2
  NAAA WILD-TYPE 258 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAAA MUTATED      1    2
  NAAA WILD-TYPE  258  219
        clus
vv       NAAA MUTATED NAAA WILD-TYPE
  FEMALE            1            258
  MALE              2            219
[1] 2 2
[1] FALSE
D279V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NAAA MUTATED                            0                                 0
  NAAA WILD-TYPE                         18                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NAAA MUTATED                                                    3
  NAAA WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NAAA MUTATED                                            0
  NAAA WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NAAA MUTATED                                               0
  NAAA WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  NAAA MUTATED                                0
  NAAA WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  NAAA MUTATED                                    0
  NAAA WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NAAA MUTATED                              0                             0
  NAAA WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NAAA MUTATED                                               0
  NAAA WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  NAAA MUTATED                              0
  NAAA WILD-TYPE                            9
D279V9, multiclass
                                                    clus
vv                                                   NAAA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   NAAA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V10, binary
                cls
clus               0   1
  NAAA MUTATED     0   3
  NAAA WILD-TYPE  20 457
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAAA MUTATED      0    3
  NAAA WILD-TYPE   20  457
     clus
vv    NAAA MUTATED NAAA WILD-TYPE
  NO             0             20
  YES            3            457
[1] 2 2
[1] FALSE
D279V11, continuous
[1] "Remove cluster labels:" "NAAA MUTATED"          
clus
  NAAA MUTATED NAAA WILD-TYPE 
             2            331 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4396 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4397     TCGA-05-4398     TCGA-05-4405     TCGA-05-4410 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4415     TCGA-05-4417     TCGA-05-4418     TCGA-05-4420 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4422     TCGA-05-4424     TCGA-05-4425     TCGA-05-4426 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4430     TCGA-05-4432     TCGA-05-4433 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4434     TCGA-05-5420     TCGA-05-5423     TCGA-05-5425 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-5428     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-4629     TCGA-38-4631 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-7271     TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3398     TCGA-44-3918     TCGA-44-4112 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-5643     TCGA-44-5644     TCGA-44-5645     TCGA-44-6144 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6148     TCGA-44-6774 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6775     TCGA-44-6776     TCGA-44-6777     TCGA-44-6778 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6779     TCGA-44-7659     TCGA-44-7660     TCGA-44-7661 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-7662     TCGA-44-7667     TCGA-44-7669     TCGA-44-7670 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-7672     TCGA-44-8117     TCGA-44-8119     TCGA-44-8120 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B     TCGA-44-A47F 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU     TCGA-49-4486 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4490     TCGA-49-4494     TCGA-49-4505 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4507     TCGA-49-4510     TCGA-49-4514 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-49-6745 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-6761     TCGA-49-6767     TCGA-50-5051     TCGA-50-5072 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5939     TCGA-50-5941     TCGA-50-5942 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-6590     TCGA-50-7109     TCGA-50-8457     TCGA-50-8459 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6543     TCGA-55-6971     TCGA-55-6983     TCGA-55-6985 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7281     TCGA-55-7283     TCGA-55-7574     TCGA-55-7724 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7728     TCGA-55-7903 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8089     TCGA-55-8092 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8203 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8208     TCGA-55-8299     TCGA-55-8301 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8302     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8614     TCGA-55-8615     TCGA-55-8620 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A491     TCGA-55-A492     TCGA-55-A493 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG     TCGA-62-8398 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-8399     TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A46S     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-1676     TCGA-64-1677     TCGA-64-1679     TCGA-64-5774 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-5815     TCGA-69-7761     TCGA-69-7763     TCGA-69-7764 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-7973     TCGA-69-7974     TCGA-69-7978     TCGA-69-7979 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-7980     TCGA-69-8253     TCGA-69-8254     TCGA-69-8255 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-69-A59K     TCGA-73-4658     TCGA-73-4659     TCGA-73-4662 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4666     TCGA-73-4668     TCGA-73-4670     TCGA-73-4675 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-75-5122     TCGA-75-5125 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-5126     TCGA-75-6203     TCGA-75-6206     TCGA-75-6207 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-6211     TCGA-75-6214     TCGA-75-7027     TCGA-75-7031 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7145     TCGA-78-7146     TCGA-78-7147     TCGA-78-7148 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7149     TCGA-78-7150     TCGA-78-7152     TCGA-78-7153 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7154     TCGA-78-7155     TCGA-78-7156     TCGA-78-7158 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7159     TCGA-78-7160     TCGA-78-7161     TCGA-78-7162 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7163     TCGA-78-7166     TCGA-78-7167     TCGA-78-7220 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7535     TCGA-78-7536     TCGA-78-7537     TCGA-78-7539 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-80-5608     TCGA-80-5611     TCGA-83-5908     TCGA-86-6851 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7714     TCGA-86-7954 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8673     TCGA-86-8674     TCGA-91-6829 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-6830     TCGA-91-6835     TCGA-91-6836     TCGA-91-6840 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC     TCGA-93-7347 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-7039     TCGA-95-7043     TCGA-95-7562     TCGA-95-7944 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-7947     TCGA-95-7948     TCGA-95-A4VK     TCGA-95-A4VN 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-A4VP     TCGA-97-7546     TCGA-97-7547     TCGA-97-7552 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7937     TCGA-97-7938 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-7941     TCGA-97-8171     TCGA-97-8172     TCGA-97-8174 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-8176     TCGA-97-8179     TCGA-97-A4LX     TCGA-97-A4M0 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-A4M1     TCGA-97-A4M2     TCGA-97-A4M3     TCGA-97-A4M5 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025     TCGA-99-8028 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-99-8032     TCGA-J2-8194     TCGA-J2-A4AD     TCGA-J2-A4AG 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-L4-A4E5     TCGA-L4-A4E6     TCGA-L9-A443     TCGA-L9-A444 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY     TCGA-MP-A4T2 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7     TCGA-MP-A4T8 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TD 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YF     TCGA-NJ-A4YG 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-NJ-A4YI     TCGA-NJ-A4YP     TCGA-NJ-A4YQ     TCGA-NJ-A55A 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-NJ-A55O     TCGA-NJ-A55R     TCGA-O1-A52J 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
D279V12, continuous
                vv
clus              R0  R1  R2  RX
  NAAA MUTATED     1   0   0   0
  NAAA WILD-TYPE 309  11   4  25
D279V13, multiclass
[1] "Remove cluster labels:" "NAAA MUTATED"          
clus
  NAAA MUTATED NAAA WILD-TYPE 
             1            349 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-4123 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-4627 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-4628     TCGA-38-4629     TCGA-38-4630     TCGA-38-4631 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F     TCGA-44-2657 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-2661     TCGA-44-2665     TCGA-44-3396     TCGA-44-3398 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-3918     TCGA-44-3919     TCGA-44-4112     TCGA-44-6144 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4486 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4488     TCGA-49-4494     TCGA-49-4501 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4507     TCGA-49-4510 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-4512     TCGA-49-4514     TCGA-49-6742     TCGA-49-6744 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-49-6761     TCGA-49-6767     TCGA-50-5051     TCGA-50-5055 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-5066     TCGA-50-5931     TCGA-50-5942     TCGA-50-5944 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-50-6593     TCGA-50-6597     TCGA-50-6673     TCGA-50-8460 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-1592 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-5899     TCGA-55-6642     TCGA-55-6970     TCGA-55-6971 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6972     TCGA-55-6980     TCGA-55-6981     TCGA-55-6983 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-6985     TCGA-55-7281     TCGA-55-7284     TCGA-55-7570 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7727     TCGA-55-7728     TCGA-55-7815 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7903     TCGA-55-7907     TCGA-55-7910     TCGA-55-7911 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-7914     TCGA-55-7994     TCGA-55-7995     TCGA-55-8085 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8087     TCGA-55-8089     TCGA-55-8090     TCGA-55-8091 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8097     TCGA-55-8203 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8204     TCGA-55-8205     TCGA-55-8206     TCGA-55-8207 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8505     TCGA-55-8506     TCGA-55-8507     TCGA-55-8508 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8510     TCGA-55-8511     TCGA-55-8512     TCGA-55-8513 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8614     TCGA-55-8615     TCGA-55-8616 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-55-A4DG     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1676     TCGA-64-1677     TCGA-64-1679 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5774     TCGA-64-5775     TCGA-64-5778 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-64-5779     TCGA-64-5781     TCGA-64-5815     TCGA-67-3771 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-67-3773     TCGA-67-4679     TCGA-67-6215     TCGA-67-6216 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-67-6217     TCGA-71-6725     TCGA-71-8520     TCGA-73-4658 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-4677 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-75-5125 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-5126     TCGA-75-5146     TCGA-75-5147     TCGA-75-6203 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-6205     TCGA-75-6206     TCGA-75-6207     TCGA-75-6211 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-6212     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-75-7030     TCGA-75-7031     TCGA-78-7143     TCGA-78-7145 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7540 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-80-5608     TCGA-80-5611     TCGA-83-5908     TCGA-86-6562 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-7953     TCGA-86-7954     TCGA-86-7955     TCGA-86-8054 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8073     TCGA-86-8074 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8075     TCGA-86-8076     TCGA-86-8278     TCGA-86-8279 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8280     TCGA-86-8358     TCGA-86-8359     TCGA-86-8585 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-8672 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-8673     TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6828     TCGA-91-6829     TCGA-91-6835 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-91-6840     TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-93-A4JQ     TCGA-95-7562     TCGA-95-7944     TCGA-95-7947 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-95-7948     TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7554     TCGA-97-7938     TCGA-97-7941 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-97-8176     TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-99-8033 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-L4-A4E6     TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4SY     TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TC     TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" "NAAA WILD-TYPE" 
    TCGA-NJ-A4YQ 
"NAAA WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAAA MUTATED                                  0     0
  NAAA WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NAAA MUTATED                           1     2
  NAAA WILD-TYPE                        28   375
D279V14, multiclass
                                  clus
vv                                 NAAA MUTATED NAAA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       2            375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V15, binary
                cls
clus               0   1
  NAAA MUTATED     0   3
  NAAA WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAAA MUTATED      0    3
  NAAA WILD-TYPE    6  346
                        clus
vv                       NAAA MUTATED NAAA WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(280) Variable = GART MUTATION ANALYSIS
D280V1, survival
                sevent
clus2              0   1
  GART MUTATED     4   2
  GART WILD-TYPE 311 139
  GART MUTATED GART WILD-TYPE 
             6            450 
  GART MUTATED GART WILD-TYPE 
             2            139 
$`GART MUTATED`
TCGA-44-3918 TCGA-44-7660 TCGA-55-8620 TCGA-86-8672 TCGA-97-8174 TCGA-MN-A4N1 
       34.06        19.46         2.17         0.62         5.39        27.19 

$`GART WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        38.24         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        14.60        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67        17.92        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  GART MUTATED GART WILD-TYPE 
          0.62           0.00 
  GART MUTATED GART WILD-TYPE 
         34.06         223.96 
  GART MUTATED GART WILD-TYPE 
        12.425         18.030 
[1] "0.6 - 34.1 (12.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.9"
D280V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GART MUTATED         0        1        1         2         1          0
  GART WILD-TYPE       4      122      132        44        66         70
                vv
clus             STAGE IIIB STAGE IV
  GART MUTATED            0        1
  GART WILD-TYPE         11       24
D280V3, multiclass
            clus
vv           GART MUTATED GART WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              1            132
  STAGE IIA             2             44
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GART MUTATED     2   3   1   0
  GART WILD-TYPE 153 258  42  18
D280V4, multiclass
    clus
vv   GART MUTATED GART WILD-TYPE
  T1            2            153
  T2            3            258
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  GART MUTATED     4   2     0
  GART WILD-TYPE 303  87    72
D280V5, multiclass
       clus
vv      GART MUTATED GART WILD-TYPE
  N0               4            303
  N1               2             87
  N2+N3            0             72
[1] 3 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
  GART MUTATED     4   1
  GART WILD-TYPE 323  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GART MUTATED      4    1
  GART WILD-TYPE  323   22
   clus
vv  GART MUTATED GART WILD-TYPE
  0            4            323
  1            1             22
[1] 2 2
[1] FALSE
D280V7, binary
                cls
clus               0   1
  GART MUTATED     1   5
  GART WILD-TYPE 258 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  GART MUTATED      1    5
  GART WILD-TYPE  258  216
        clus
vv       GART MUTATED GART WILD-TYPE
  FEMALE            1            258
  MALE              5            216
[1] 2 2
[1] FALSE
D280V8, continuous
[1] "Remove cluster labels:" "GART MUTATED"          
clus
  GART MUTATED GART WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-A48Z     TCGA-55-A490 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" "GART WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"GART WILD-TYPE" "GART WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GART MUTATED                            0                                 0
  GART WILD-TYPE                         18                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GART MUTATED                                                    5
  GART WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GART MUTATED                                            0
  GART WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GART MUTATED                                               0
  GART WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  GART MUTATED                                0
  GART WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  GART MUTATED                                    0
  GART WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GART MUTATED                              0                             1
  GART WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GART MUTATED                                               0
  GART WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  GART MUTATED                              0
  GART WILD-TYPE                            9
D280V9, multiclass
                                                    clus
vv                                                   GART MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   GART WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V10, binary
                cls
clus               0   1
  GART MUTATED     0   6
  GART WILD-TYPE  20 454
[1] "tbl2"
                cls
clus             [,1] [,2]
  GART MUTATED      0    6
  GART WILD-TYPE   20  454
     clus
vv    GART MUTATED GART WILD-TYPE
  NO             0             20
  YES            6            454
[1] 2 2
[1] FALSE
D280V11, continuous
D280V12, continuous
                vv
clus              R0  R1  R2  RX
  GART MUTATED     4   0   0   0
  GART WILD-TYPE 306  11   4  25
D280V13, multiclass
    clus
vv   GART MUTATED GART WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GART MUTATED                                  0     0
  GART WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GART MUTATED                           1     5
  GART WILD-TYPE                        28   372
D280V14, multiclass
                                  clus
vv                                 GART MUTATED GART WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V15, binary
                cls
clus               0   1
  GART MUTATED     0   6
  GART WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  GART MUTATED      0    6
  GART WILD-TYPE    6  343
                        clus
vv                       GART MUTATED GART WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(281) Variable = TARBP1 MUTATION ANALYSIS
D281V1, survival
                  sevent
clus2                0   1
  TARBP1 MUTATED    12   1
  TARBP1 WILD-TYPE 303 140
  TARBP1 MUTATED TARBP1 WILD-TYPE 
              13              443 
  TARBP1 MUTATED TARBP1 WILD-TYPE 
               1              140 
$`TARBP1 MUTATED`
TCGA-05-4424 TCGA-05-5428 TCGA-38-4626 TCGA-55-6712 TCGA-55-7227 TCGA-55-7726 
       30.02        22.03       120.79         0.79         1.74         1.28 
TCGA-55-7995 TCGA-55-8506 TCGA-78-7148 TCGA-86-8076 TCGA-95-7567 TCGA-95-7947 
        0.16         0.36        20.58        16.08        18.67        15.68 
TCGA-MP-A4TH 
       14.66 

$`TARBP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68        97.74        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       23.05        48.62         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        15.75        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        1.22         2.86        12.39        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
       31.23         2.43        10.09        29.46        11.05        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  TARBP1 MUTATED TARBP1 WILD-TYPE 
            0.16             0.00 
  TARBP1 MUTATED TARBP1 WILD-TYPE 
          120.79           223.96 
  TARBP1 MUTATED TARBP1 WILD-TYPE 
           15.68            18.12 
[1] "0.2 - 120.8 (15.7)" "0.0 - 224.0 (18.1)"
[1] "hr=" "3.6"
D281V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TARBP1 MUTATED         0        5        0         3         4          2
  TARBP1 WILD-TYPE       4      118      133        43        63         68
                  vv
clus               STAGE IIIB STAGE IV
  TARBP1 MUTATED            0        0
  TARBP1 WILD-TYPE         11       25
D281V3, multiclass
            clus
vv           TARBP1 MUTATED TARBP1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              118
  STAGE IB                0              133
  STAGE IIA               3               43
  STAGE IIB               4               63
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TARBP1 MUTATED     6   4   4   0
  TARBP1 WILD-TYPE 149 257  39  18
D281V4, multiclass
    clus
vv   TARBP1 MUTATED TARBP1 WILD-TYPE
  T1              6              149
  T2              4              257
  T3              4               39
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  TARBP1 MUTATED     8   5     1
  TARBP1 WILD-TYPE 299  84    71
D281V5, multiclass
       clus
vv      TARBP1 MUTATED TARBP1 WILD-TYPE
  N0                 8              299
  N1                 5               84
  N2+N3              1               71
[1] 3 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
  TARBP1 MUTATED    10   0
  TARBP1 WILD-TYPE 317  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TARBP1 MUTATED     10    0
  TARBP1 WILD-TYPE  317   23
   clus
vv  TARBP1 MUTATED TARBP1 WILD-TYPE
  0             10              317
  1              0               23
[1] 2 2
[1] FALSE
D281V7, binary
                  cls
clus                 0   1
  TARBP1 MUTATED     6   8
  TARBP1 WILD-TYPE 253 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TARBP1 MUTATED      6    8
  TARBP1 WILD-TYPE  253  213
        clus
vv       TARBP1 MUTATED TARBP1 WILD-TYPE
  FEMALE              6              253
  MALE                8              213
[1] 2 2
[1] FALSE
D281V8, continuous
[1] "Remove cluster labels:" "TARBP1 MUTATED"        
clus
  TARBP1 MUTATED TARBP1 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" "TARBP1 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TARBP1 MUTATED                            0                                 5
  TARBP1 WILD-TYPE                         18                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TARBP1 MUTATED                                                    7
  TARBP1 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TARBP1 MUTATED                                            0
  TARBP1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TARBP1 MUTATED                                               0
  TARBP1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TARBP1 MUTATED                                0
  TARBP1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TARBP1 MUTATED                                    0
  TARBP1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TARBP1 MUTATED                              0                             2
  TARBP1 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TARBP1 MUTATED                                               0
  TARBP1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TARBP1 MUTATED                              0
  TARBP1 WILD-TYPE                            9
D281V9, multiclass
                                                    clus
vv                                                   TARBP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   TARBP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V10, binary
                  cls
clus                 0   1
  TARBP1 MUTATED     0  14
  TARBP1 WILD-TYPE  20 446
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TARBP1 MUTATED      0   14
  TARBP1 WILD-TYPE   20  446
     clus
vv    TARBP1 MUTATED TARBP1 WILD-TYPE
  NO               0               20
  YES             14              446
[1] 2 2
[1] FALSE
D281V11, continuous
D281V12, continuous
                  vv
clus                R0  R1  R2  RX
  TARBP1 MUTATED     9   1   1   0
  TARBP1 WILD-TYPE 301  10   3  25
D281V13, multiclass
    clus
vv   TARBP1 MUTATED TARBP1 WILD-TYPE
  R0              9              301
  R1              1               10
  R2              1                3
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TARBP1 MUTATED                                  0     0
  TARBP1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TARBP1 MUTATED                           0    11
  TARBP1 WILD-TYPE                        29   366
D281V14, multiclass
                                  clus
vv                                 TARBP1 MUTATED TARBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        11              366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V15, binary
                  cls
clus                 0   1
  TARBP1 MUTATED     0   9
  TARBP1 WILD-TYPE   6 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TARBP1 MUTATED      0    9
  TARBP1 WILD-TYPE    6  340
                        clus
vv                       TARBP1 MUTATED TARBP1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              9              340
[1] 2 2
[1] FALSE

Clustering(282) Variable = HLA-DQA2 MUTATION ANALYSIS
D282V1, survival
                    sevent
clus2                  0   1
  HLA-DQA2 MUTATED     3   0
  HLA-DQA2 WILD-TYPE 312 141
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
                 3                453 
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
                 0                141 
$`HLA-DQA2 MUTATED`
TCGA-49-6744 TCGA-69-7978 TCGA-91-A4BC 
       29.26         2.30         1.45 

$`HLA-DQA2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.18        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
              1.45               0.00 
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
             29.26             223.96 
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
              2.30              18.08 
[1] "1.4 - 29.3 (2.3)"   "0.0 - 224.0 (18.1)"
[1] "hr="     "1200000"
D282V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HLA-DQA2 MUTATED         0        0        0         2         1          0
  HLA-DQA2 WILD-TYPE       4      123      133        44        66         70
                    vv
clus                 STAGE IIIB STAGE IV
  HLA-DQA2 MUTATED            0        0
  HLA-DQA2 WILD-TYPE         11       25
D282V3, multiclass
            clus
vv           HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                123
  STAGE IB                  0                133
  STAGE IIA                 2                 44
  STAGE IIB                 1                 66
  STAGE IIIA                0                 70
  STAGE IIIB                0                 11
  STAGE IV                  0                 25
[1] 8 2
[1] TRUE
[1] "dimension of 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-DQA2 MUTATED     0   3   0   0
  HLA-DQA2 WILD-TYPE 155 258  43  18
D282V4, multiclass
    clus
vv   HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE
  T1                0                155
  T2                3                258
  T3                0                 43
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  HLA-DQA2 MUTATED     1   2     0
  HLA-DQA2 WILD-TYPE 306  87    72
D282V5, multiclass
       clus
vv      HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE
  N0                   1                306
  N1                   2                 87
  N2+N3                0                 72
[1] 3 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
  HLA-DQA2 MUTATED     0   0
  HLA-DQA2 WILD-TYPE 327  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DQA2 MUTATED      0    0
  HLA-DQA2 WILD-TYPE  327   23
D282V7, binary
                    cls
clus                   0   1
  HLA-DQA2 MUTATED     1   2
  HLA-DQA2 WILD-TYPE 258 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DQA2 MUTATED      1    2
  HLA-DQA2 WILD-TYPE  258  219
        clus
vv       HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE
  FEMALE                1                258
  MALE                  2                219
[1] 2 2
[1] FALSE
D282V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  HLA-DQA2 MUTATED                            0
  HLA-DQA2 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  HLA-DQA2 MUTATED                                   2
  HLA-DQA2 WILD-TYPE                               100
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HLA-DQA2 MUTATED                                                    1
  HLA-DQA2 WILD-TYPE                                                293
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HLA-DQA2 MUTATED                                            0
  HLA-DQA2 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HLA-DQA2 MUTATED                                               0
  HLA-DQA2 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  HLA-DQA2 MUTATED                                0
  HLA-DQA2 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  HLA-DQA2 MUTATED                                    0
  HLA-DQA2 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HLA-DQA2 MUTATED                              0                             0
  HLA-DQA2 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HLA-DQA2 MUTATED                                               0
  HLA-DQA2 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  HLA-DQA2 MUTATED                              0
  HLA-DQA2 WILD-TYPE                            9
D282V9, multiclass
                                                    clus
vv                                                   HLA-DQA2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   HLA-DQA2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V10, binary
                    cls
clus                   0   1
  HLA-DQA2 MUTATED     0   3
  HLA-DQA2 WILD-TYPE  20 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DQA2 MUTATED      0    3
  HLA-DQA2 WILD-TYPE   20  457
     clus
vv    HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE
  NO                 0                 20
  YES                3                457
[1] 2 2
[1] FALSE
D282V11, continuous
D282V12, continuous
[1] "Remove cluster labels:" "HLA-DQA2 MUTATED"      
clus
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
                 1                256 
        TCGA-05-4384         TCGA-05-4390         TCGA-05-4396 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4405         TCGA-05-4410         TCGA-05-4415 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4417         TCGA-05-4424         TCGA-05-4427 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4433         TCGA-05-5420         TCGA-05-5423 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-5425         TCGA-05-5428         TCGA-35-4122 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-35-4123         TCGA-35-5375         TCGA-38-4625 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-38-4626         TCGA-38-7271         TCGA-38-A44F 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-2656         TCGA-44-2657         TCGA-44-3396 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-4112 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-5644         TCGA-44-5645         TCGA-44-6144 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-6145         TCGA-44-6147         TCGA-44-6148 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-6774         TCGA-44-6775         TCGA-44-6776 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-6777         TCGA-44-6778         TCGA-44-6779 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-7659         TCGA-44-7660         TCGA-44-7661 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-7662         TCGA-44-7667         TCGA-44-7669 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-7670         TCGA-44-7672         TCGA-44-8117 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-8119         TCGA-44-8120         TCGA-44-A479 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-A47A         TCGA-44-A47B         TCGA-44-A47F 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-A47G         TCGA-44-A4SS         TCGA-44-A4SU 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-49-4486         TCGA-49-4494         TCGA-49-4505 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-53-7624         TCGA-53-7626         TCGA-53-7813 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-1592         TCGA-55-1595 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-5899         TCGA-55-6642         TCGA-55-6712 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-6971         TCGA-55-7227         TCGA-55-7283 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7570         TCGA-55-7574         TCGA-55-7576 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7724         TCGA-55-7725         TCGA-55-7726 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7728         TCGA-55-7907         TCGA-55-7910 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7911         TCGA-55-7914         TCGA-55-8089 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8092         TCGA-55-8094         TCGA-55-8096 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8097         TCGA-55-8205         TCGA-55-8299 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8301         TCGA-55-8302         TCGA-55-8506 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8507         TCGA-55-8511         TCGA-55-8512 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8514         TCGA-55-8615         TCGA-55-8620 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8621         TCGA-55-A48X         TCGA-55-A48Y 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-A48Z         TCGA-55-A490         TCGA-55-A491 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-A492         TCGA-55-A493         TCGA-55-A494 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-62-8398         TCGA-64-1677         TCGA-64-1681 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-64-5774         TCGA-64-5775         TCGA-64-5778 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-64-5779         TCGA-64-5781         TCGA-69-7761 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-69-7763         TCGA-69-7764         TCGA-69-7765 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-69-7974         TCGA-69-7979         TCGA-69-8253 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-69-8255         TCGA-69-A59K         TCGA-73-4659 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-73-4662         TCGA-73-4666         TCGA-73-4668 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-73-4670         TCGA-73-4675         TCGA-73-4676 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-73-7498         TCGA-75-6214         TCGA-75-7025 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-75-7027         TCGA-75-7031         TCGA-78-7145 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7146         TCGA-78-7147         TCGA-78-7148 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7149         TCGA-78-7150         TCGA-78-7152 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7153         TCGA-78-7154         TCGA-78-7155 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7156         TCGA-78-7158         TCGA-78-7159 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7160         TCGA-78-7161         TCGA-78-7162 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7163         TCGA-78-7166         TCGA-78-7167 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7220         TCGA-78-7535         TCGA-78-7536 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7537         TCGA-78-7539         TCGA-78-7542 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7633         TCGA-78-8640         TCGA-78-8648 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-8655         TCGA-78-8660         TCGA-78-8662 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-80-5607         TCGA-80-5608         TCGA-83-5908 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-6851         TCGA-86-7711         TCGA-86-7714 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-7954         TCGA-86-8054         TCGA-86-8055 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8056         TCGA-86-8073         TCGA-86-8074 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8281         TCGA-86-8358         TCGA-86-8359 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8669         TCGA-86-8673         TCGA-86-8674 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-A456         TCGA-91-6829         TCGA-91-6830 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-91-6836         TCGA-91-6840         TCGA-91-6849 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-91-8499         TCGA-93-7347         TCGA-93-7348 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-93-8067         TCGA-93-A4JN         TCGA-93-A4JO 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-93-A4JQ         TCGA-95-7043         TCGA-95-7562 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-95-7567         TCGA-95-7944         TCGA-95-7947 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-95-7948         TCGA-95-A4VK         TCGA-95-A4VN 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-95-A4VP         TCGA-97-7546         TCGA-97-7553 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-97-7554         TCGA-97-7941         TCGA-97-8171 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-97-8172         TCGA-97-8174         TCGA-97-8176 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-97-8179         TCGA-97-A4LX         TCGA-97-A4M0 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-97-A4M1         TCGA-97-A4M2         TCGA-97-A4M3 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-97-A4M5         TCGA-97-A4M7         TCGA-99-7458 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-99-8025         TCGA-99-8028         TCGA-99-8032 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-J2-8194         TCGA-J2-A4AD         TCGA-J2-A4AG 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-L4-A4E5         TCGA-L4-A4E6         TCGA-L9-A443 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-L9-A444         TCGA-MN-A4N1         TCGA-MN-A4N4 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MN-A4N5         TCGA-MP-A4SV         TCGA-MP-A4SW 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4T2         TCGA-MP-A4T4         TCGA-MP-A4T7 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4T8         TCGA-MP-A4T9         TCGA-MP-A4TA 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4TC         TCGA-MP-A4TE         TCGA-MP-A4TF 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4TH         TCGA-MP-A4TI         TCGA-MP-A4TK 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A5C7         TCGA-NJ-A4YG         TCGA-NJ-A4YI 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-O1-A52J 
"HLA-DQA2 WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  HLA-DQA2 MUTATED     1   0   0   0
  HLA-DQA2 WILD-TYPE 309  11   4  25
D282V13, multiclass
[1] "Remove cluster labels:" "HLA-DQA2 MUTATED"      
clus
  HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE 
                 1                349 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4382         TCGA-05-4384         TCGA-05-4389 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4390         TCGA-05-4395         TCGA-05-4396 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4397         TCGA-05-4398         TCGA-05-4402 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4403         TCGA-05-4405         TCGA-05-4410 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4415         TCGA-05-4417         TCGA-05-4418 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4420         TCGA-05-4422         TCGA-05-4424 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4425         TCGA-05-4426         TCGA-05-4427 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4430         TCGA-05-4432         TCGA-05-4433 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-4434         TCGA-05-5420         TCGA-05-5423 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-5425         TCGA-05-5428         TCGA-05-5429 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-05-5715         TCGA-35-4122         TCGA-35-4123 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-35-5375         TCGA-38-4625         TCGA-38-4626 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-38-4627         TCGA-38-4628         TCGA-38-4629 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-38-4630         TCGA-38-4631         TCGA-38-4632 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-38-6178         TCGA-38-7271         TCGA-38-A44F 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-2657         TCGA-44-2661         TCGA-44-2665 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-3396         TCGA-44-3398         TCGA-44-3918 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-44-6144 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-6148         TCGA-44-6775         TCGA-44-A479 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-A47A         TCGA-44-A47B         TCGA-44-A47G 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-44-A4SU         TCGA-49-4486         TCGA-49-4487 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-49-4488         TCGA-49-4494         TCGA-49-4501 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-49-4505         TCGA-49-4506         TCGA-49-4507 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-49-4510         TCGA-49-4512         TCGA-49-4514 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-49-6742         TCGA-49-6761         TCGA-49-6767 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-50-5051         TCGA-50-5055         TCGA-50-5066 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-50-5931         TCGA-50-5942         TCGA-50-5944 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-50-6593         TCGA-50-6597         TCGA-50-6673 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-50-8460         TCGA-53-7624         TCGA-53-7626 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-1592         TCGA-55-5899 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-6642         TCGA-55-6970         TCGA-55-6971 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-6972         TCGA-55-6980         TCGA-55-6981 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-6983         TCGA-55-6985         TCGA-55-7281 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7284         TCGA-55-7570         TCGA-55-7574 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7576         TCGA-55-7724         TCGA-55-7725 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7726         TCGA-55-7727         TCGA-55-7728 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7815         TCGA-55-7903         TCGA-55-7907 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7910         TCGA-55-7911         TCGA-55-7914 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-7994         TCGA-55-7995         TCGA-55-8085 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8087         TCGA-55-8089         TCGA-55-8090 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8091         TCGA-55-8092         TCGA-55-8094 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8097         TCGA-55-8203         TCGA-55-8204 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8205         TCGA-55-8206         TCGA-55-8207 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8299         TCGA-55-8301 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8302         TCGA-55-8505         TCGA-55-8506 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8507         TCGA-55-8508         TCGA-55-8510 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8513 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8514         TCGA-55-8614         TCGA-55-8615 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8616         TCGA-55-8619         TCGA-55-8620 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-8621         TCGA-55-A48X         TCGA-55-A48Y 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-A48Z         TCGA-55-A490         TCGA-55-A491 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-A492         TCGA-55-A493         TCGA-55-A494 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-55-A4DF         TCGA-55-A4DG         TCGA-62-8394 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-62-8395         TCGA-62-8397         TCGA-62-8398 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-62-8399         TCGA-62-8402         TCGA-62-A46O 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-62-A46P         TCGA-62-A46R         TCGA-62-A46S 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-62-A46U         TCGA-62-A46V         TCGA-62-A46Y 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-62-A470         TCGA-62-A471         TCGA-62-A472 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1679 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-64-1681         TCGA-64-5774         TCGA-64-5775 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-64-5778         TCGA-64-5779         TCGA-64-5781 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-64-5815         TCGA-67-3771         TCGA-67-3773 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-67-4679         TCGA-67-6215         TCGA-67-6216 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-67-6217         TCGA-71-6725         TCGA-71-8520 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-73-4658         TCGA-73-4659         TCGA-73-4662 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-73-4666         TCGA-73-4668         TCGA-73-4670 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-73-4675         TCGA-73-4676         TCGA-73-4677 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-73-7498         TCGA-73-7499         TCGA-75-5122 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-75-5125         TCGA-75-5126         TCGA-75-5146 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-75-5147         TCGA-75-6203         TCGA-75-6205 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-75-6206         TCGA-75-6207         TCGA-75-6211 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-75-6212         TCGA-75-6214         TCGA-75-7025 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-75-7027         TCGA-75-7030         TCGA-75-7031 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7143         TCGA-78-7145         TCGA-78-7146 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7147         TCGA-78-7148         TCGA-78-7149 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7150         TCGA-78-7152         TCGA-78-7153 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7154         TCGA-78-7155         TCGA-78-7156 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7158         TCGA-78-7159         TCGA-78-7160 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7161         TCGA-78-7162         TCGA-78-7163 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7166         TCGA-78-7167         TCGA-78-7220 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7535         TCGA-78-7536         TCGA-78-7537 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7539         TCGA-78-7540         TCGA-78-7542 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-7633         TCGA-78-8640         TCGA-78-8648 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-78-8655         TCGA-78-8660         TCGA-78-8662 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-80-5607         TCGA-80-5608         TCGA-80-5611 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-83-5908         TCGA-86-6562         TCGA-86-7701 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-7711         TCGA-86-7713         TCGA-86-7714 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-7953         TCGA-86-7954         TCGA-86-7955 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8054         TCGA-86-8055         TCGA-86-8056 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8073         TCGA-86-8074         TCGA-86-8075 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8076         TCGA-86-8278         TCGA-86-8279 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8280         TCGA-86-8358         TCGA-86-8359 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8585         TCGA-86-8668         TCGA-86-8669 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8671         TCGA-86-8672         TCGA-86-8673 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-8674         TCGA-86-A456         TCGA-86-A4JF 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-86-A4P7         TCGA-91-6828         TCGA-91-6829 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-91-6835         TCGA-91-6840         TCGA-91-A4BD 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-93-7347         TCGA-93-7348         TCGA-93-8067 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-93-A4JN         TCGA-93-A4JO         TCGA-93-A4JP 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-93-A4JQ         TCGA-95-7562         TCGA-95-7944 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-95-7947         TCGA-95-7948         TCGA-95-8039 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-95-A4VK         TCGA-95-A4VN         TCGA-97-7546 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-97-7554         TCGA-97-7938         TCGA-97-7941 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-97-8176         TCGA-97-A4M2         TCGA-97-A4M7 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-99-7458         TCGA-99-8025         TCGA-99-8028 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-99-8032         TCGA-99-8033         TCGA-J2-A4AD 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-J2-A4AE         TCGA-J2-A4AG         TCGA-L4-A4E5 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-L4-A4E6         TCGA-L9-A443         TCGA-L9-A444 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MN-A4N1         TCGA-MN-A4N4         TCGA-MN-A4N5 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4SV         TCGA-MP-A4SW         TCGA-MP-A4SY 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4T2         TCGA-MP-A4T4         TCGA-MP-A4T6 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4T7         TCGA-MP-A4T8         TCGA-MP-A4T9 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4TA         TCGA-MP-A4TC         TCGA-MP-A4TD 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4TE         TCGA-MP-A4TF         TCGA-MP-A4TH 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-MP-A4TI         TCGA-MP-A4TK         TCGA-MP-A5C7 
"HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" "HLA-DQA2 WILD-TYPE" 
        TCGA-NJ-A4YQ 
"HLA-DQA2 WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-DQA2 MUTATED                                  0     0
  HLA-DQA2 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HLA-DQA2 MUTATED                           0     3
  HLA-DQA2 WILD-TYPE                        29   374
D282V14, multiclass
                                  clus
vv                                 HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       0                 29
  WHITE                                           3                374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V15, binary
                    cls
clus                   0   1
  HLA-DQA2 MUTATED     0   2
  HLA-DQA2 WILD-TYPE   6 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DQA2 MUTATED      0    2
  HLA-DQA2 WILD-TYPE    6  347
                        clus
vv                       HLA-DQA2 MUTATED HLA-DQA2 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                2                347
[1] 2 2
[1] FALSE

Clustering(283) Variable = AHDC1 MUTATION ANALYSIS
D283V1, survival
                 sevent
clus2               0   1
  AHDC1 MUTATED     9   0
  AHDC1 WILD-TYPE 306 141
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              9             447 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              0             141 
$`AHDC1 MUTATED`
TCGA-35-5375 TCGA-44-A47B TCGA-55-8506 TCGA-64-1676 TCGA-64-5778 TCGA-86-8358 
        8.68         9.44         0.36        56.81        42.90        21.47 
TCGA-86-8673 TCGA-93-8067 TCGA-MN-A4N4 
       14.96         6.12        38.63 

$`AHDC1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         5.98        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.98        15.32        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       20.65        55.43        38.37        87.98         2.04        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       16.08        15.65        15.85        23.05        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82         9.76         4.18        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  AHDC1 MUTATED AHDC1 WILD-TYPE 
           0.36            0.00 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
          56.81          223.96 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
          14.96           18.08 
[1] "0.4 - 56.8 (15.0)"  "0.0 - 224.0 (18.1)"
[1] "hr="     "9200000"
D283V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AHDC1 MUTATED         0        2        5         0         1          1
  AHDC1 WILD-TYPE       4      121      128        46        66         69
                 vv
clus              STAGE IIIB STAGE IV
  AHDC1 MUTATED            0        1
  AHDC1 WILD-TYPE         11       24
D283V3, multiclass
            clus
vv           AHDC1 MUTATED AHDC1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               5             128
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AHDC1 MUTATED     2   7   1   0
  AHDC1 WILD-TYPE 153 254  42  18
D283V4, multiclass
    clus
vv   AHDC1 MUTATED AHDC1 WILD-TYPE
  T1             2             153
  T2             7             254
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  AHDC1 MUTATED     8   0     2
  AHDC1 WILD-TYPE 299  89    70
D283V5, multiclass
       clus
vv      AHDC1 MUTATED AHDC1 WILD-TYPE
  N0                8             299
  N1                0              89
  N2+N3             2              70
[1] 3 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
  AHDC1 MUTATED     7   1
  AHDC1 WILD-TYPE 320  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      7    1
  AHDC1 WILD-TYPE  320   22
   clus
vv  AHDC1 MUTATED AHDC1 WILD-TYPE
  0             7             320
  1             1              22
[1] 2 2
[1] FALSE
D283V7, binary
                 cls
clus                0   1
  AHDC1 MUTATED     1   9
  AHDC1 WILD-TYPE 258 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      1    9
  AHDC1 WILD-TYPE  258  212
        clus
vv       AHDC1 MUTATED AHDC1 WILD-TYPE
  FEMALE             1             258
  MALE               9             212
[1] 2 2
[1] FALSE
D283V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AHDC1 MUTATED                            0                                 0
  AHDC1 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AHDC1 MUTATED                                                    8
  AHDC1 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AHDC1 MUTATED                                            0
  AHDC1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AHDC1 MUTATED                                               2
  AHDC1 WILD-TYPE                                            17
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  AHDC1 MUTATED                                0
  AHDC1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  AHDC1 MUTATED                                    0
  AHDC1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  AHDC1 MUTATED                              0                             0
  AHDC1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AHDC1 MUTATED                                               0
  AHDC1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  AHDC1 MUTATED                              0
  AHDC1 WILD-TYPE                            9
D283V9, multiclass
                                                    clus
vv                                                   AHDC1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  2
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   AHDC1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   17
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V10, binary
                 cls
clus                0   1
  AHDC1 MUTATED     0  10
  AHDC1 WILD-TYPE  20 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      0   10
  AHDC1 WILD-TYPE   20  450
     clus
vv    AHDC1 MUTATED AHDC1 WILD-TYPE
  NO              0              20
  YES            10             450
[1] 2 2
[1] FALSE
D283V11, continuous
D283V12, continuous
                 vv
clus               R0  R1  R2  RX
  AHDC1 MUTATED     8   0   0   2
  AHDC1 WILD-TYPE 302  11   4  23
D283V13, multiclass
    clus
vv   AHDC1 MUTATED AHDC1 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHDC1 MUTATED                                  0     1
  AHDC1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AHDC1 MUTATED                           0     8
  AHDC1 WILD-TYPE                        29   369
D283V14, multiclass
                                  clus
vv                                 AHDC1 MUTATED AHDC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V15, binary
                 cls
clus                0   1
  AHDC1 MUTATED     0   9
  AHDC1 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      0    9
  AHDC1 WILD-TYPE    6  340
                        clus
vv                       AHDC1 MUTATED AHDC1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(284) Variable = ARHGEF12 MUTATION ANALYSIS
D284V1, survival
                    sevent
clus2                  0   1
  ARHGEF12 MUTATED    18   3
  ARHGEF12 WILD-TYPE 297 138
  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE 
                21                435 
  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE 
                 3                138 
$`ARHGEF12 MUTATED`
TCGA-05-4397 TCGA-05-4402 TCGA-05-4420 TCGA-05-4432 TCGA-05-5715 TCGA-44-2657 
       24.03         8.02        29.98        25.02         2.04        13.15 
TCGA-44-3918 TCGA-44-5644 TCGA-44-7660 TCGA-44-8117 TCGA-50-5066 TCGA-55-6982 
       34.06        28.37        19.46        12.66        31.04        32.71 
TCGA-55-8205 TCGA-55-8507 TCGA-55-8621 TCGA-55-A494 TCGA-69-8254 TCGA-73-4666 
        1.08         0.26        16.93        15.81        13.45        26.30 
TCGA-95-7039 TCGA-MN-A4N4 TCGA-NJ-A4YG 
        1.12        38.63        62.60 

$`ARHGEF12 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        0.00         9.96        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       29.00        22.03         9.04         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        38.24         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        14.60        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.00        17.59        23.64         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
       20.52        71.47        70.55        15.72        60.16        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
        2.20        45.34        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65        17.98         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61         2.17        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59         0.92        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       12.56        14.01         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE 
              0.26               0.00 
  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE 
             62.60             223.96 
  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE 
             19.46              17.98 
[1] "0.3 - 62.6 (19.5)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.9"
D284V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARHGEF12 MUTATED         0        4        9         0         5          0
  ARHGEF12 WILD-TYPE       4      119      124        46        62         70
                    vv
clus                 STAGE IIIB STAGE IV
  ARHGEF12 MUTATED            0        2
  ARHGEF12 WILD-TYPE         11       23
D284V3, multiclass
            clus
vv           ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  4                119
  STAGE IB                  9                124
  STAGE IIA                 0                 46
  STAGE IIB                 5                 62
  STAGE IIIA                0                 70
  STAGE IIIB                0                 11
  STAGE IV                  2                 23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF12 MUTATED     5  15   1   0
  ARHGEF12 WILD-TYPE 150 246  42  18
D284V4, multiclass
    clus
vv   ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  T1                5                150
  T2               15                246
  T3                1                 42
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  ARHGEF12 MUTATED    15   3     0
  ARHGEF12 WILD-TYPE 292  86    72
D284V5, multiclass
       clus
vv      ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  N0                  15                292
  N1                   3                 86
  N2+N3                0                 72
[1] 3 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
  ARHGEF12 MUTATED    12   2
  ARHGEF12 WILD-TYPE 315  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF12 MUTATED     12    2
  ARHGEF12 WILD-TYPE  315   21
   clus
vv  ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  0               12                315
  1                2                 21
[1] 2 2
[1] FALSE
D284V7, binary
                    cls
clus                   0   1
  ARHGEF12 MUTATED    12   9
  ARHGEF12 WILD-TYPE 247 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF12 MUTATED     12    9
  ARHGEF12 WILD-TYPE  247  212
        clus
vv       ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  FEMALE               12                247
  MALE                  9                212
[1] 2 2
[1] FALSE
D284V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  ARHGEF12 MUTATED                            0
  ARHGEF12 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARHGEF12 MUTATED                                   8
  ARHGEF12 WILD-TYPE                                94
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF12 MUTATED                                                   13
  ARHGEF12 WILD-TYPE                                                281
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARHGEF12 MUTATED                                            0
  ARHGEF12 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARHGEF12 MUTATED                                               0
  ARHGEF12 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  ARHGEF12 MUTATED                                0
  ARHGEF12 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  ARHGEF12 MUTATED                                    0
  ARHGEF12 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARHGEF12 MUTATED                              0                             0
  ARHGEF12 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARHGEF12 MUTATED                                               0
  ARHGEF12 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  ARHGEF12 MUTATED                              0
  ARHGEF12 WILD-TYPE                            9
D284V9, multiclass
                                                    clus
vv                                                   ARHGEF12 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   ARHGEF12 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V10, binary
                    cls
clus                   0   1
  ARHGEF12 MUTATED     1  20
  ARHGEF12 WILD-TYPE  19 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF12 MUTATED      1   20
  ARHGEF12 WILD-TYPE   19  440
     clus
vv    ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  NO                 1                 19
  YES               20                440
[1] 2 2
[1] FALSE
D284V11, continuous
D284V12, continuous
                    vv
clus                  R0  R1  R2  RX
  ARHGEF12 MUTATED    13   0   1   0
  ARHGEF12 WILD-TYPE 297  11   3  25
D284V13, multiclass
    clus
vv   ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  R0               13                297
  R1                0                 11
  R2                1                  3
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF12 MUTATED                                  0     0
  ARHGEF12 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF12 MUTATED                           1    15
  ARHGEF12 WILD-TYPE                        28   362
D284V14, multiclass
                                  clus
vv                                 ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       1                 28
  WHITE                                          15                362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V15, binary
                    cls
clus                   0   1
  ARHGEF12 MUTATED     0  14
  ARHGEF12 WILD-TYPE   6 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF12 MUTATED      0   14
  ARHGEF12 WILD-TYPE    6  335
                        clus
vv                       ARHGEF12 MUTATED ARHGEF12 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               14                335
[1] 2 2
[1] FALSE

Clustering(285) Variable = UHRF1BP1L MUTATION ANALYSIS
D285V1, survival
                     sevent
clus2                   0   1
  UHRF1BP1L MUTATED    11   5
  UHRF1BP1L WILD-TYPE 304 136
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 16                 440 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                  5                 136 
$`UHRF1BP1L MUTATED`
TCGA-05-4382 TCGA-05-4395 TCGA-44-7669 TCGA-44-8119 TCGA-50-5930 TCGA-50-6595 
       19.96         0.00        18.87         3.25         9.27         6.21 
TCGA-55-7995 TCGA-55-8085 TCGA-69-A59K TCGA-73-4668 TCGA-78-7147 TCGA-86-8280 
        0.16        29.72         7.04        15.35        19.27        23.05 
TCGA-86-8358 TCGA-86-8673 TCGA-95-7567 TCGA-NJ-A4YF 
       21.47        14.96        18.67        71.05 

$`UHRF1BP1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
       50.07         3.98        14.01        45.01        37.02         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       29.00        17.59        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.22        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 
       42.35         3.91        25.55        11.05        12.16        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 
        6.48        17.65         6.15        19.82        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       16.08        15.65        15.85        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       30.84        27.58         0.62        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         1.22         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
               0.00                0.07 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
              71.05              223.96 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
              17.01               18.03 
[1] "0.0 - 71.0 (17.0)"  "0.1 - 224.0 (18.0)"
[1] "hr=" "1.5"
D285V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  UHRF1BP1L MUTATED         0        3        3         2         5          2
  UHRF1BP1L WILD-TYPE       4      120      130        44        62         68
                     vv
clus                  STAGE IIIB STAGE IV
  UHRF1BP1L MUTATED            1        0
  UHRF1BP1L WILD-TYPE         10       25
D285V3, multiclass
            clus
vv           UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  STAGE I                    0                   4
  STAGE IA                   3                 120
  STAGE IB                   3                 130
  STAGE IIA                  2                  44
  STAGE IIB                  5                  62
  STAGE IIIA                 2                  68
  STAGE IIIB                 1                  10
  STAGE IV                   0                  25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  UHRF1BP1L MUTATED     4   9   2   1
  UHRF1BP1L WILD-TYPE 151 252  41  17
D285V4, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  T1                 4                 151
  T2                 9                 252
  T3                 2                  41
  T4                 1                  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"
                     vv
clus                   N0  N1 N2+N3
  UHRF1BP1L MUTATED     9   4     3
  UHRF1BP1L WILD-TYPE 298  85    69
D285V5, multiclass
       clus
vv      UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  N0                    9                 298
  N1                    4                  85
  N2+N3                 3                  69
[1] 3 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
  UHRF1BP1L MUTATED    15   0
  UHRF1BP1L WILD-TYPE 312  23
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     15    0
  UHRF1BP1L WILD-TYPE  312   23
   clus
vv  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  0                15                 312
  1                 0                  23
[1] 2 2
[1] FALSE
D285V7, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED     7   9
  UHRF1BP1L WILD-TYPE 252 212
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED      7    9
  UHRF1BP1L WILD-TYPE  252  212
        clus
vv       UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  FEMALE                 7                 252
  MALE                   9                 212
[1] 2 2
[1] FALSE
D285V8, continuous
[1] "Remove cluster labels:" "UHRF1BP1L MUTATED"     
clus
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                  2                  82 
         TCGA-35-4122          TCGA-35-4123          TCGA-35-5375 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-53-A4EZ          TCGA-55-7283          TCGA-55-7573 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-55-7725          TCGA-55-7910          TCGA-55-7914 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-55-8089          TCGA-55-8096          TCGA-55-8205 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-55-8208          TCGA-55-8507          TCGA-55-8508 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-55-8511          TCGA-55-8512          TCGA-55-8619 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-55-8620          TCGA-55-A48Z          TCGA-55-A490 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-55-A494          TCGA-62-8394          TCGA-62-8395 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-62-8397          TCGA-62-8398          TCGA-62-8399 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-62-8402          TCGA-62-A46O          TCGA-62-A46P 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-62-A46R          TCGA-62-A46S          TCGA-62-A46U 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-62-A46V          TCGA-62-A46Y          TCGA-62-A470 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-62-A471          TCGA-62-A472          TCGA-64-1677 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-64-1681          TCGA-64-5778          TCGA-69-7974 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-69-8254          TCGA-71-6725          TCGA-71-8520 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-73-4659          TCGA-73-4662          TCGA-73-4666 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-73-4676          TCGA-73-7498          TCGA-73-7499 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-75-5122          TCGA-83-5908          TCGA-86-7701 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-86-7711          TCGA-86-7713          TCGA-86-7714 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-86-7954          TCGA-86-7955          TCGA-86-8055 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-86-8056          TCGA-86-8074          TCGA-86-8075 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-86-8076          TCGA-86-8278          TCGA-86-8279 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-86-8281          TCGA-86-8359          TCGA-86-8668 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-86-8669          TCGA-86-8671          TCGA-86-A4JF 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-86-A4P7          TCGA-91-6849          TCGA-93-7348 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-93-8067          TCGA-93-A4JN          TCGA-93-A4JO 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-99-7458          TCGA-MN-A4N1          TCGA-MN-A4N4 
"UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" "UHRF1BP1L WILD-TYPE" 
         TCGA-MN-A4N5 
"UHRF1BP1L WILD-TYPE" 
                     vv
clus                  LUNG ACINAR ADENOCARCINOMA
  UHRF1BP1L MUTATED                            0
  UHRF1BP1L WILD-TYPE                         18
                     vv
clus                  LUNG ADENOCARCINOMA MIXED SUBTYPE
  UHRF1BP1L MUTATED                                   6
  UHRF1BP1L WILD-TYPE                                96
                     vv
clus                  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  UHRF1BP1L MUTATED                                                    6
  UHRF1BP1L WILD-TYPE                                                288
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  UHRF1BP1L MUTATED                                            0
  UHRF1BP1L WILD-TYPE                                          4
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  UHRF1BP1L MUTATED                                               2
  UHRF1BP1L WILD-TYPE                                            17
                     vv
clus                  LUNG CLEAR CELL ADENOCARCINOMA
  UHRF1BP1L MUTATED                                0
  UHRF1BP1L WILD-TYPE                              2
                     vv
clus                  LUNG MICROPAPILLARY ADENOCARCINOMA
  UHRF1BP1L MUTATED                                    1
  UHRF1BP1L WILD-TYPE                                  2
                     vv
clus                  LUNG MUCINOUS ADENOCARCINOMA
  UHRF1BP1L MUTATED                              0
  UHRF1BP1L WILD-TYPE                            2
                     vv
clus                  LUNG PAPILLARY ADENOCARCINOMA
  UHRF1BP1L MUTATED                               1
  UHRF1BP1L WILD-TYPE                            21
                     vv
clus                  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  UHRF1BP1L MUTATED                                               0
  UHRF1BP1L WILD-TYPE                                             5
                     vv
clus                  MUCINOUS (COLLOID) CARCINOMA
  UHRF1BP1L MUTATED                              0
  UHRF1BP1L WILD-TYPE                            9
D285V9, multiclass
                                                    clus
vv                                                   UHRF1BP1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                         0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      2
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       0
  LUNG PAPILLARY ADENOCARCINOMA                                      1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      0
  MUCINOUS (COLLOID) CARCINOMA                                       0
                                                    clus
vv                                                   UHRF1BP1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                   96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                           4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                       17
  LUNG CLEAR CELL ADENOCARCINOMA                                       2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                   2
  LUNG MUCINOUS ADENOCARCINOMA                                         2
  LUNG PAPILLARY ADENOCARCINOMA                                       21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                        5
  MUCINOUS (COLLOID) CARCINOMA                                         9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V10, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED     1  15
  UHRF1BP1L WILD-TYPE  19 445
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED      1   15
  UHRF1BP1L WILD-TYPE   19  445
     clus
vv    UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  NO                  1                  19
  YES                15                 445
[1] 2 2
[1] FALSE
D285V11, continuous
D285V12, continuous
                     vv
clus                   R0  R1  R2  RX
  UHRF1BP1L MUTATED     9   0   0   0
  UHRF1BP1L WILD-TYPE 301  11   4  25
D285V13, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  R0                 9                 301
  R1                 0                  11
  R2                 0                   4
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UHRF1BP1L MUTATED                                  1     0
  UHRF1BP1L WILD-TYPE                                0     7
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  UHRF1BP1L MUTATED                           3    10
  UHRF1BP1L WILD-TYPE                        26   367
D285V14, multiclass
                                  clus
vv                                 UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 1                   0
  ASIAN                                            0                   7
  BLACK OR AFRICAN AMERICAN                        3                  26
  WHITE                                           10                 367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V15, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED     0  13
  UHRF1BP1L WILD-TYPE   6 336
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED      0   13
  UHRF1BP1L WILD-TYPE    6  336
                        clus
vv                       UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  HISPANIC OR LATINO                     0                   6
  NOT HISPANIC OR LATINO                13                 336
[1] 2 2
[1] FALSE

Clustering(286) Variable = HERC3 MUTATION ANALYSIS
D286V1, survival
                 sevent
clus2               0   1
  HERC3 MUTATED     6   2
  HERC3 WILD-TYPE 309 139
  HERC3 MUTATED HERC3 WILD-TYPE 
              8             448 
  HERC3 MUTATED HERC3 WILD-TYPE 
              2             139 
$`HERC3 MUTATED`
TCGA-05-4418 TCGA-05-5425 TCGA-49-4514 TCGA-55-8208 TCGA-55-8511 TCGA-69-7974 
        9.01        29.00        55.89        22.16         0.30         6.05 
TCGA-MP-A4TC TCGA-NJ-A55O 
        2.43         0.43 

$`HERC3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
        0.95         0.36         0.26         0.49        17.72         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26        19.82        59.11 

  HERC3 MUTATED HERC3 WILD-TYPE 
            0.3             0.0 
  HERC3 MUTATED HERC3 WILD-TYPE 
          55.89          223.96 
  HERC3 MUTATED HERC3 WILD-TYPE 
           7.53           18.10 
[1] "0.3 - 55.9 (7.5)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D286V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HERC3 MUTATED         0        2        1         1         1          3
  HERC3 WILD-TYPE       4      121      132        45        66         67
                 vv
clus              STAGE IIIB STAGE IV
  HERC3 MUTATED            0        0
  HERC3 WILD-TYPE         11       25
D286V3, multiclass
            clus
vv           HERC3 MUTATED HERC3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               1             132
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HERC3 MUTATED     4   3   1   0
  HERC3 WILD-TYPE 151 258  42  18
D286V4, multiclass
    clus
vv   HERC3 MUTATED HERC3 WILD-TYPE
  T1             4             151
  T2             3             258
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  HERC3 MUTATED     3   2     3
  HERC3 WILD-TYPE 304  87    69
D286V5, multiclass
       clus
vv      HERC3 MUTATED HERC3 WILD-TYPE
  N0                3             304
  N1                2              87
  N2+N3             3              69
[1] 3 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
  HERC3 MUTATED     6   0
  HERC3 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC3 MUTATED      6    0
  HERC3 WILD-TYPE  321   23
   clus
vv  HERC3 MUTATED HERC3 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D286V7, binary
                 cls
clus                0   1
  HERC3 MUTATED     5   3
  HERC3 WILD-TYPE 254 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC3 MUTATED      5    3
  HERC3 WILD-TYPE  254  218
        clus
vv       HERC3 MUTATED HERC3 WILD-TYPE
  FEMALE             5             254
  MALE               3             218
[1] 2 2
[1] FALSE
D286V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HERC3 MUTATED                            0                                 3
  HERC3 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HERC3 MUTATED                                                    3
  HERC3 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HERC3 MUTATED                                            0
  HERC3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HERC3 MUTATED                                               0
  HERC3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HERC3 MUTATED                                0
  HERC3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HERC3 MUTATED                                    0
  HERC3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HERC3 MUTATED                              0                             1
  HERC3 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HERC3 MUTATED                                               0
  HERC3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HERC3 MUTATED                              1
  HERC3 WILD-TYPE                            8
D286V9, multiclass
                                                    clus
vv                                                   HERC3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   HERC3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V10, binary
                 cls
clus                0   1
  HERC3 MUTATED     1   7
  HERC3 WILD-TYPE  19 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC3 MUTATED      1    7
  HERC3 WILD-TYPE   19  453
     clus
vv    HERC3 MUTATED HERC3 WILD-TYPE
  NO              1              19
  YES             7             453
[1] 2 2
[1] FALSE
D286V11, continuous
D286V12, continuous
                 vv
clus               R0  R1  R2  RX
  HERC3 MUTATED     6   0   0   0
  HERC3 WILD-TYPE 304  11   4  25
D286V13, multiclass
    clus
vv   HERC3 MUTATED HERC3 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HERC3 MUTATED                                  0     0
  HERC3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HERC3 MUTATED                           0     6
  HERC3 WILD-TYPE                        29   371
D286V14, multiclass
                                  clus
vv                                 HERC3 MUTATED HERC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V15, binary
                 cls
clus                0   1
  HERC3 MUTATED     0   5
  HERC3 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC3 MUTATED      0    5
  HERC3 WILD-TYPE    6  344
                        clus
vv                       HERC3 MUTATED HERC3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(287) Variable = GALNT14 MUTATION ANALYSIS
D287V1, survival
                   sevent
clus2                 0   1
  GALNT14 MUTATED    14   5
  GALNT14 WILD-TYPE 301 136
  GALNT14 MUTATED GALNT14 WILD-TYPE 
               19               437 
  GALNT14 MUTATED GALNT14 WILD-TYPE 
                5               136 
$`GALNT14 MUTATED`
TCGA-05-4382 TCGA-05-4420 TCGA-49-4506 TCGA-50-5049 TCGA-50-6593 TCGA-55-1595 
       19.96        29.98        32.84        70.55        11.05        48.62 
TCGA-55-7994 TCGA-55-8299 TCGA-55-8506 TCGA-69-7979 TCGA-73-4670 TCGA-78-8662 
       19.82        15.42         0.36         2.93         4.31       110.50 
TCGA-86-6851 TCGA-86-8073 TCGA-86-8359 TCGA-97-7546 TCGA-99-8025 TCGA-MN-A4N5 
        5.88        24.33        14.60        31.69        34.85         2.76 
TCGA-NJ-A55O 
        0.43 

$`GALNT14 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        46.72        14.07         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        71.47        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       22.55        42.35         3.91        25.55        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 
       34.29        30.54        13.94         9.21        23.05         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       10.55        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        21.47         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19        38.63        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26        19.82        59.11 

  GALNT14 MUTATED GALNT14 WILD-TYPE 
             0.36              0.00 
  GALNT14 MUTATED GALNT14 WILD-TYPE 
           110.50            223.96 
  GALNT14 MUTATED GALNT14 WILD-TYPE 
            19.82             17.98 
[1] "0.4 - 110.5 (19.8)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.4"
D287V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GALNT14 MUTATED         0        5        5         2         3          4
  GALNT14 WILD-TYPE       4      118      128        44        64         66
                   vv
clus                STAGE IIIB STAGE IV
  GALNT14 MUTATED            0        1
  GALNT14 WILD-TYPE         11       24
D287V3, multiclass
            clus
vv           GALNT14 MUTATED GALNT14 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 5               118
  STAGE IB                 5               128
  STAGE IIA                2                44
  STAGE IIB                3                64
  STAGE IIIA               4                66
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GALNT14 MUTATED     7   9   4   0
  GALNT14 WILD-TYPE 148 252  39  18
D287V4, multiclass
    clus
vv   GALNT14 MUTATED GALNT14 WILD-TYPE
  T1               7               148
  T2               9               252
  T3               4                39
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  GALNT14 MUTATED    13   3     4
  GALNT14 WILD-TYPE 294  86    68
D287V5, multiclass
       clus
vv      GALNT14 MUTATED GALNT14 WILD-TYPE
  N0                 13               294
  N1                  3                86
  N2+N3               4                68
[1] 3 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
  GALNT14 MUTATED    14   1
  GALNT14 WILD-TYPE 313  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT14 MUTATED     14    1
  GALNT14 WILD-TYPE  313   22
   clus
vv  GALNT14 MUTATED GALNT14 WILD-TYPE
  0              14               313
  1               1                22
[1] 2 2
[1] FALSE
D287V7, binary
                   cls
clus                  0   1
  GALNT14 MUTATED    13   7
  GALNT14 WILD-TYPE 246 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT14 MUTATED     13    7
  GALNT14 WILD-TYPE  246  214
        clus
vv       GALNT14 MUTATED GALNT14 WILD-TYPE
  FEMALE              13               246
  MALE                 7               214
[1] 2 2
[1] FALSE
D287V8, continuous
[1] "Remove cluster labels:" "GALNT14 MUTATED"       
clus
  GALNT14 MUTATED GALNT14 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4 
"GALNT14 WILD-TYPE" "GALNT14 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  GALNT14 MUTATED                            2
  GALNT14 WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  GALNT14 MUTATED                                   4
  GALNT14 WILD-TYPE                                98
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GALNT14 MUTATED                                                   11
  GALNT14 WILD-TYPE                                                283
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GALNT14 MUTATED                                            0
  GALNT14 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GALNT14 MUTATED                                               1
  GALNT14 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  GALNT14 MUTATED                                1
  GALNT14 WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  GALNT14 MUTATED                                    0
  GALNT14 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GALNT14 MUTATED                              0                             0
  GALNT14 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GALNT14 MUTATED                                               0
  GALNT14 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  GALNT14 MUTATED                              1
  GALNT14 WILD-TYPE                            8
D287V9, multiclass
                                                    clus
vv                                                   GALNT14 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   GALNT14 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V10, binary
                   cls
clus                  0   1
  GALNT14 MUTATED     1  19
  GALNT14 WILD-TYPE  19 441
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT14 MUTATED      1   19
  GALNT14 WILD-TYPE   19  441
     clus
vv    GALNT14 MUTATED GALNT14 WILD-TYPE
  NO                1                19
  YES              19               441
[1] 2 2
[1] FALSE
D287V11, continuous
D287V12, continuous
                   vv
clus                 R0  R1  R2  RX
  GALNT14 MUTATED    14   1   0   0
  GALNT14 WILD-TYPE 296  10   4  25
D287V13, multiclass
    clus
vv   GALNT14 MUTATED GALNT14 WILD-TYPE
  R0              14               296
  R1               1                10
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GALNT14 MUTATED                                  0     1
  GALNT14 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GALNT14 MUTATED                           1    14
  GALNT14 WILD-TYPE                        28   363
D287V14, multiclass
                                  clus
vv                                 GALNT14 MUTATED GALNT14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                         14               363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V15, binary
                   cls
clus                  0   1
  GALNT14 MUTATED     0  16
  GALNT14 WILD-TYPE   6 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT14 MUTATED      0   16
  GALNT14 WILD-TYPE    6  333
                        clus
vv                       GALNT14 MUTATED GALNT14 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              16               333
[1] 2 2
[1] FALSE

Clustering(288) Variable = FLT4 MUTATION ANALYSIS
D288V1, survival
                sevent
clus2              0   1
  FLT4 MUTATED     9   6
  FLT4 WILD-TYPE 306 135
  FLT4 MUTATED FLT4 WILD-TYPE 
            15            441 
  FLT4 MUTATED FLT4 WILD-TYPE 
             6            135 
$`FLT4 MUTATED`
TCGA-05-4397 TCGA-05-4398 TCGA-05-4424 TCGA-38-4632 TCGA-44-2657 TCGA-50-5931 
       24.03        47.05        30.02        44.61        13.15        14.27 
TCGA-50-5933 TCGA-50-6594 TCGA-55-1595 TCGA-55-6985 TCGA-55-6987 TCGA-69-7974 
       78.67        12.16        48.62        40.54        70.26         6.05 
TCGA-78-7220 TCGA-95-7039 TCGA-NJ-A4YQ 
       26.53         1.12        29.13 

$`FLT4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        0.00         9.96         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        29.98        12.00        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        40.60        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       24.99       107.21         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13         1.64         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  FLT4 MUTATED FLT4 WILD-TYPE 
          1.12           0.00 
  FLT4 MUTATED FLT4 WILD-TYPE 
         78.67         223.96 
  FLT4 MUTATED FLT4 WILD-TYPE 
         29.13          17.75 
[1] "1.1 - 78.7 (29.1)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.2"
D288V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FLT4 MUTATED         0        4        5         0         3          3
  FLT4 WILD-TYPE       4      119      128        46        64         67
                vv
clus             STAGE IIIB STAGE IV
  FLT4 MUTATED            2        1
  FLT4 WILD-TYPE          9       24
D288V3, multiclass
            clus
vv           FLT4 MUTATED FLT4 WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              5            128
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            3             67
  STAGE IIIB            2              9
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLT4 MUTATED     4   9   3   2
  FLT4 WILD-TYPE 151 252  40  16
D288V4, multiclass
    clus
vv   FLT4 MUTATED FLT4 WILD-TYPE
  T1            4            151
  T2            9            252
  T3            3             40
  T4            2             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"
                vv
clus              N0  N1 N2+N3
  FLT4 MUTATED     9   2     5
  FLT4 WILD-TYPE 298  87    67
D288V5, multiclass
       clus
vv      FLT4 MUTATED FLT4 WILD-TYPE
  N0               9            298
  N1               2             87
  N2+N3            5             67
[1] 3 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
  FLT4 MUTATED    13   1
  FLT4 WILD-TYPE 314  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT4 MUTATED     13    1
  FLT4 WILD-TYPE  314   22
   clus
vv  FLT4 MUTATED FLT4 WILD-TYPE
  0           13            314
  1            1             22
[1] 2 2
[1] FALSE
D288V7, binary
                cls
clus               0   1
  FLT4 MUTATED    11   7
  FLT4 WILD-TYPE 248 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT4 MUTATED     11    7
  FLT4 WILD-TYPE  248  214
        clus
vv       FLT4 MUTATED FLT4 WILD-TYPE
  FEMALE           11            248
  MALE              7            214
[1] 2 2
[1] FALSE
D288V8, continuous
[1] "Remove cluster labels:" "FLT4 MUTATED"          
clus
  FLT4 MUTATED FLT4 WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8358     TCGA-86-8359 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"FLT4 WILD-TYPE" "FLT4 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FLT4 MUTATED                            0                                 7
  FLT4 WILD-TYPE                         18                                95
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FLT4 MUTATED                                                   10
  FLT4 WILD-TYPE                                                284
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FLT4 MUTATED                                            0
  FLT4 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FLT4 MUTATED                                               0
  FLT4 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  FLT4 MUTATED                                1
  FLT4 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  FLT4 MUTATED                                    0
  FLT4 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FLT4 MUTATED                              0                             0
  FLT4 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FLT4 MUTATED                                               0
  FLT4 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  FLT4 MUTATED                              0
  FLT4 WILD-TYPE                            9
D288V9, multiclass
                                                    clus
vv                                                   FLT4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   FLT4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V10, binary
                cls
clus               0   1
  FLT4 MUTATED     3  15
  FLT4 WILD-TYPE  17 445
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT4 MUTATED      3   15
  FLT4 WILD-TYPE   17  445
     clus
vv    FLT4 MUTATED FLT4 WILD-TYPE
  NO             3             17
  YES           15            445
[1] 2 2
[1] FALSE
D288V11, continuous
D288V12, continuous
                vv
clus              R0  R1  R2  RX
  FLT4 MUTATED     8   1   0   2
  FLT4 WILD-TYPE 302  10   4  23
D288V13, multiclass
    clus
vv   FLT4 MUTATED FLT4 WILD-TYPE
  R0            8            302
  R1            1             10
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLT4 MUTATED                                  0     1
  FLT4 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLT4 MUTATED                           2    11
  FLT4 WILD-TYPE                        27   366
D288V14, multiclass
                                  clus
vv                                 FLT4 MUTATED FLT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                      11            366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V15, binary
                cls
clus               0   1
  FLT4 MUTATED     0  12
  FLT4 WILD-TYPE   6 337
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT4 MUTATED      0   12
  FLT4 WILD-TYPE    6  337
                        clus
vv                       FLT4 MUTATED FLT4 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           12            337
[1] 2 2
[1] FALSE

Clustering(289) Variable = ACBD5 MUTATION ANALYSIS
D289V1, survival
                 sevent
clus2               0   1
  ACBD5 MUTATED    10   1
  ACBD5 WILD-TYPE 305 140
  ACBD5 MUTATED ACBD5 WILD-TYPE 
             11             445 
  ACBD5 MUTATED ACBD5 WILD-TYPE 
              1             140 
$`ACBD5 MUTATED`
TCGA-05-4389 TCGA-44-7661 TCGA-44-7662 TCGA-44-A4SS TCGA-50-5935 TCGA-55-8302 
       45.01        12.03         7.17        13.64        21.47         0.76 
TCGA-55-8621 TCGA-86-8358 TCGA-86-8585 TCGA-95-8039 TCGA-L9-A444 
       16.93        21.47         1.15        27.29         0.20 

$`ACBD5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        14.60        19.46        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU 
       15.98        15.32         9.44        11.08        11.54        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       15.85        23.05        14.60        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.65         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ACBD5 MUTATED ACBD5 WILD-TYPE 
            0.2             0.0 
  ACBD5 MUTATED ACBD5 WILD-TYPE 
          45.01          223.96 
  ACBD5 MUTATED ACBD5 WILD-TYPE 
          13.64           18.12 
[1] "0.2 - 45.0 (13.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.1"
D289V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ACBD5 MUTATED         0        6        5         0         0          0
  ACBD5 WILD-TYPE       4      117      128        46        67         70
                 vv
clus              STAGE IIIB STAGE IV
  ACBD5 MUTATED            0        0
  ACBD5 WILD-TYPE         11       25
D289V3, multiclass
            clus
vv           ACBD5 MUTATED ACBD5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               6             117
  STAGE IB               5             128
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACBD5 MUTATED     6   5   0   0
  ACBD5 WILD-TYPE 149 256  43  18
D289V4, multiclass
    clus
vv   ACBD5 MUTATED ACBD5 WILD-TYPE
  T1             6             149
  T2             5             256
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ACBD5 MUTATED    11   0     0
  ACBD5 WILD-TYPE 296  89    72
D289V5, multiclass
       clus
vv      ACBD5 MUTATED ACBD5 WILD-TYPE
  N0               11             296
  N1                0              89
  N2+N3             0              72
[1] 3 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
  ACBD5 MUTATED     6   0
  ACBD5 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD5 MUTATED      6    0
  ACBD5 WILD-TYPE  321   23
   clus
vv  ACBD5 MUTATED ACBD5 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D289V7, binary
                 cls
clus                0   1
  ACBD5 MUTATED     4   7
  ACBD5 WILD-TYPE 255 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD5 MUTATED      4    7
  ACBD5 WILD-TYPE  255  214
        clus
vv       ACBD5 MUTATED ACBD5 WILD-TYPE
  FEMALE             4             255
  MALE               7             214
[1] 2 2
[1] FALSE
D289V8, continuous
[1] "Remove cluster labels:" "ACBD5 MUTATED"         
clus
  ACBD5 MUTATED ACBD5 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" "ACBD5 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ACBD5 MUTATED                            1                                 1
  ACBD5 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ACBD5 MUTATED                                                    8
  ACBD5 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ACBD5 MUTATED                                            0
  ACBD5 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ACBD5 MUTATED                                               0
  ACBD5 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ACBD5 MUTATED                                0
  ACBD5 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ACBD5 MUTATED                                    0
  ACBD5 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ACBD5 MUTATED                              0                             0
  ACBD5 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ACBD5 MUTATED                                               1
  ACBD5 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ACBD5 MUTATED                              0
  ACBD5 WILD-TYPE                            9
D289V9, multiclass
                                                    clus
vv                                                   ACBD5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ACBD5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V10, binary
                 cls
clus                0   1
  ACBD5 MUTATED     1  10
  ACBD5 WILD-TYPE  19 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD5 MUTATED      1   10
  ACBD5 WILD-TYPE   19  450
     clus
vv    ACBD5 MUTATED ACBD5 WILD-TYPE
  NO              1              19
  YES            10             450
[1] 2 2
[1] FALSE
D289V11, continuous
D289V12, continuous
                 vv
clus               R0  R1  R2  RX
  ACBD5 MUTATED     6   0   0   1
  ACBD5 WILD-TYPE 304  11   4  24
D289V13, multiclass
    clus
vv   ACBD5 MUTATED ACBD5 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACBD5 MUTATED                                  0     0
  ACBD5 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACBD5 MUTATED                           0    10
  ACBD5 WILD-TYPE                        29   367
D289V14, multiclass
                                  clus
vv                                 ACBD5 MUTATED ACBD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V15, binary
                 cls
clus                0   1
  ACBD5 MUTATED     0   9
  ACBD5 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD5 MUTATED      0    9
  ACBD5 WILD-TYPE    6  340
                        clus
vv                       ACBD5 MUTATED ACBD5 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(290) Variable = CARD6 MUTATION ANALYSIS
D290V1, survival
                 sevent
clus2               0   1
  CARD6 MUTATED     8   5
  CARD6 WILD-TYPE 307 136
  CARD6 MUTATED CARD6 WILD-TYPE 
             13             443 
  CARD6 MUTATED CARD6 WILD-TYPE 
              5             136 
$`CARD6 MUTATED`
TCGA-05-5425 TCGA-44-8119 TCGA-50-5946 TCGA-53-7624 TCGA-55-5899 TCGA-55-8299 
       29.00         3.25        22.55        34.29         2.86        15.42 
TCGA-64-5775 TCGA-78-7536 TCGA-78-8640 TCGA-86-7711 TCGA-86-8278 TCGA-MN-A4N4 
        2.04         8.02       214.62        34.39        15.65        38.63 
TCGA-NJ-A55R 
       19.82 

$`CARD6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
       31.20        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       15.75        16.08        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        59.11 

  CARD6 MUTATED CARD6 WILD-TYPE 
           2.04            0.00 
  CARD6 MUTATED CARD6 WILD-TYPE 
         214.62          223.96 
  CARD6 MUTATED CARD6 WILD-TYPE 
          19.82           17.98 
[1] "2.0 - 214.6 (19.8)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1"  
D290V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CARD6 MUTATED         0        5        1         2         3          2
  CARD6 WILD-TYPE       4      118      132        44        64         68
                 vv
clus              STAGE IIIB STAGE IV
  CARD6 MUTATED            0        1
  CARD6 WILD-TYPE         11       24
D290V3, multiclass
            clus
vv           CARD6 MUTATED CARD6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               1             132
  STAGE IIA              2              44
  STAGE IIB              3              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CARD6 MUTATED     6   6   1   1
  CARD6 WILD-TYPE 149 255  42  17
D290V4, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  T1             6             149
  T2             6             255
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  CARD6 MUTATED     8   5     1
  CARD6 WILD-TYPE 299  84    71
D290V5, multiclass
       clus
vv      CARD6 MUTATED CARD6 WILD-TYPE
  N0                8             299
  N1                5              84
  N2+N3             1              71
[1] 3 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
  CARD6 MUTATED    10   1
  CARD6 WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED     10    1
  CARD6 WILD-TYPE  317   22
   clus
vv  CARD6 MUTATED CARD6 WILD-TYPE
  0            10             317
  1             1              22
[1] 2 2
[1] FALSE
D290V7, binary
                 cls
clus                0   1
  CARD6 MUTATED     4  10
  CARD6 WILD-TYPE 255 211
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED      4   10
  CARD6 WILD-TYPE  255  211
        clus
vv       CARD6 MUTATED CARD6 WILD-TYPE
  FEMALE             4             255
  MALE              10             211
[1] 2 2
[1] FALSE
D290V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CARD6 MUTATED                            0                                 2
  CARD6 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CARD6 MUTATED                                                   12
  CARD6 WILD-TYPE                                                282
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CARD6 MUTATED                                            0
  CARD6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CARD6 MUTATED                                               0
  CARD6 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CARD6 MUTATED                                0
  CARD6 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CARD6 MUTATED                                    0
  CARD6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CARD6 MUTATED                              0                             0
  CARD6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CARD6 MUTATED                                               0
  CARD6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CARD6 MUTATED                              0
  CARD6 WILD-TYPE                            9
D290V9, multiclass
                                                    clus
vv                                                   CARD6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CARD6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V10, binary
                 cls
clus                0   1
  CARD6 MUTATED     1  13
  CARD6 WILD-TYPE  19 447
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED      1   13
  CARD6 WILD-TYPE   19  447
     clus
vv    CARD6 MUTATED CARD6 WILD-TYPE
  NO              1              19
  YES            13             447
[1] 2 2
[1] FALSE
D290V11, continuous
D290V12, continuous
                 vv
clus               R0  R1  R2  RX
  CARD6 MUTATED    11   0   0   0
  CARD6 WILD-TYPE 299  11   4  25
D290V13, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  R0            11             299
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CARD6 MUTATED                                  0     0
  CARD6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CARD6 MUTATED                           0    11
  CARD6 WILD-TYPE                        29   366
D290V14, multiclass
                                  clus
vv                                 CARD6 MUTATED CARD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V15, binary
                 cls
clus                0   1
  CARD6 MUTATED     2   7
  CARD6 WILD-TYPE   4 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED      2    7
  CARD6 WILD-TYPE    4  342
                        clus
vv                       CARD6 MUTATED CARD6 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(291) Variable = ANKRD44 MUTATION ANALYSIS
D291V1, survival
                   sevent
clus2                 0   1
  ANKRD44 MUTATED    10   5
  ANKRD44 WILD-TYPE 305 136
  ANKRD44 MUTATED ANKRD44 WILD-TYPE 
               15               441 
  ANKRD44 MUTATED ANKRD44 WILD-TYPE 
                5               136 
$`ANKRD44 MUTATED`
TCGA-38-4631 TCGA-38-4632 TCGA-44-6144 TCGA-49-6745 TCGA-50-5930 TCGA-50-6590 
       11.64        44.61        23.77        17.16         9.27        42.35 
TCGA-55-7227 TCGA-55-7911 TCGA-55-8506 TCGA-67-3771 TCGA-69-7761 TCGA-69-7974 
        1.74        17.65         0.36        20.05         6.12         6.05 
TCGA-95-7562 TCGA-97-A4M5 TCGA-MN-A4N4 
        2.86        20.84        38.63 

$`ANKRD44 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
      120.79        37.71        49.05        28.41        35.28        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.37        12.59        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 
       55.89        14.63        12.13        29.26        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.22        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       70.26         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64        13.87         6.64        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        1.08        19.00        17.29         1.12         1.22        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ANKRD44 MUTATED ANKRD44 WILD-TYPE 
             0.36              0.00 
  ANKRD44 MUTATED ANKRD44 WILD-TYPE 
            44.61            223.96 
  ANKRD44 MUTATED ANKRD44 WILD-TYPE 
            17.16             18.12 
[1] "0.4 - 44.6 (17.2)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.5"
D291V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ANKRD44 MUTATED         0        5        5         1         1          5
  ANKRD44 WILD-TYPE       4      118      128        45        66         65
                   vv
clus                STAGE IIIB STAGE IV
  ANKRD44 MUTATED            0        1
  ANKRD44 WILD-TYPE         11       24
D291V3, multiclass
            clus
vv           ANKRD44 MUTATED ANKRD44 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 5               118
  STAGE IB                 5               128
  STAGE IIA                1                45
  STAGE IIB                1                66
  STAGE IIIA               5                65
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD44 MUTATED     5  10   3   0
  ANKRD44 WILD-TYPE 150 251  40  18
D291V4, multiclass
    clus
vv   ANKRD44 MUTATED ANKRD44 WILD-TYPE
  T1               5               150
  T2              10               251
  T3               3                40
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  ANKRD44 MUTATED    11   3     4
  ANKRD44 WILD-TYPE 296  86    68
D291V5, multiclass
       clus
vv      ANKRD44 MUTATED ANKRD44 WILD-TYPE
  N0                 11               296
  N1                  3                86
  N2+N3               4                68
[1] 3 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
  ANKRD44 MUTATED    12   1
  ANKRD44 WILD-TYPE 315  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD44 MUTATED     12    1
  ANKRD44 WILD-TYPE  315   22
   clus
vv  ANKRD44 MUTATED ANKRD44 WILD-TYPE
  0              12               315
  1               1                22
[1] 2 2
[1] FALSE
D291V7, binary
                   cls
clus                  0   1
  ANKRD44 MUTATED     7  11
  ANKRD44 WILD-TYPE 252 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD44 MUTATED      7   11
  ANKRD44 WILD-TYPE  252  210
        clus
vv       ANKRD44 MUTATED ANKRD44 WILD-TYPE
  FEMALE               7               252
  MALE                11               210
[1] 2 2
[1] FALSE
D291V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ANKRD44 MUTATED                            1
  ANKRD44 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ANKRD44 MUTATED                                   3
  ANKRD44 WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ANKRD44 MUTATED                                                   13
  ANKRD44 WILD-TYPE                                                281
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ANKRD44 MUTATED                                            0
  ANKRD44 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ANKRD44 MUTATED                                               0
  ANKRD44 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ANKRD44 MUTATED                                0
  ANKRD44 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ANKRD44 MUTATED                                    0
  ANKRD44 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ANKRD44 MUTATED                              0                             1
  ANKRD44 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ANKRD44 MUTATED                                               0
  ANKRD44 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ANKRD44 MUTATED                              0
  ANKRD44 WILD-TYPE                            9
D291V9, multiclass
                                                    clus
vv                                                   ANKRD44 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ANKRD44 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V10, binary
                   cls
clus                  0   1
  ANKRD44 MUTATED     2  16
  ANKRD44 WILD-TYPE  18 444
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD44 MUTATED      2   16
  ANKRD44 WILD-TYPE   18  444
     clus
vv    ANKRD44 MUTATED ANKRD44 WILD-TYPE
  NO                2                18
  YES              16               444
[1] 2 2
[1] FALSE
D291V11, continuous
D291V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ANKRD44 MUTATED     8   0   1   2
  ANKRD44 WILD-TYPE 302  11   3  23
D291V13, multiclass
    clus
vv   ANKRD44 MUTATED ANKRD44 WILD-TYPE
  R0               8               302
  R1               0                11
  R2               1                 3
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD44 MUTATED                                  0     0
  ANKRD44 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD44 MUTATED                           3    12
  ANKRD44 WILD-TYPE                        26   365
D291V14, multiclass
                                  clus
vv                                 ANKRD44 MUTATED ANKRD44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      3                26
  WHITE                                         12               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V15, binary
                   cls
clus                  0   1
  ANKRD44 MUTATED     0  14
  ANKRD44 WILD-TYPE   6 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD44 MUTATED      0   14
  ANKRD44 WILD-TYPE    6  335
                        clus
vv                       ANKRD44 MUTATED ANKRD44 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              14               335
[1] 2 2
[1] FALSE

Clustering(292) Variable = DPEP2 MUTATION ANALYSIS
D292V1, survival
                 sevent
clus2               0   1
  DPEP2 MUTATED     4   2
  DPEP2 WILD-TYPE 311 139
  DPEP2 MUTATED DPEP2 WILD-TYPE 
              6             450 
  DPEP2 MUTATED DPEP2 WILD-TYPE 
              2             139 
$`DPEP2 MUTATED`
TCGA-55-1592 TCGA-55-5899 TCGA-55-7724 TCGA-62-A46Y TCGA-86-8673 TCGA-NJ-A4YQ 
       23.05         2.86        23.18        13.61        14.96        29.13 

$`DPEP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94         9.21        48.62         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1.32         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       67.96        72.30        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  DPEP2 MUTATED DPEP2 WILD-TYPE 
           2.86            0.00 
  DPEP2 MUTATED DPEP2 WILD-TYPE 
          29.13          223.96 
  DPEP2 MUTATED DPEP2 WILD-TYPE 
         19.005          18.030 
[1] "2.9 - 29.1 (19.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.7"
D292V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DPEP2 MUTATED         0        3        3         0         0          1
  DPEP2 WILD-TYPE       4      120      130        46        67         69
                 vv
clus              STAGE IIIB STAGE IV
  DPEP2 MUTATED            0        0
  DPEP2 WILD-TYPE         11       25
D292V3, multiclass
            clus
vv           DPEP2 MUTATED DPEP2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DPEP2 MUTATED     2   5   0   0
  DPEP2 WILD-TYPE 153 256  43  18
D292V4, multiclass
    clus
vv   DPEP2 MUTATED DPEP2 WILD-TYPE
  T1             2             153
  T2             5             256
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  DPEP2 MUTATED     5   1     1
  DPEP2 WILD-TYPE 302  88    71
D292V5, multiclass
       clus
vv      DPEP2 MUTATED DPEP2 WILD-TYPE
  N0                5             302
  N1                1              88
  N2+N3             1              71
[1] 3 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
  DPEP2 MUTATED     6   0
  DPEP2 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPEP2 MUTATED      6    0
  DPEP2 WILD-TYPE  321   23
   clus
vv  DPEP2 MUTATED DPEP2 WILD-TYPE
  0             6             321
  1             0              23
[1] 2 2
[1] FALSE
D292V7, binary
                 cls
clus                0   1
  DPEP2 MUTATED     3   4
  DPEP2 WILD-TYPE 256 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPEP2 MUTATED      3    4
  DPEP2 WILD-TYPE  256  217
        clus
vv       DPEP2 MUTATED DPEP2 WILD-TYPE
  FEMALE             3             256
  MALE               4             217
[1] 2 2
[1] FALSE
D292V8, continuous
[1] "Remove cluster labels:" "DPEP2 MUTATED"         
clus
  DPEP2 MUTATED DPEP2 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A470      TCGA-62-A471 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" "DPEP2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DPEP2 MUTATED                            0                                 1
  DPEP2 WILD-TYPE                         18                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DPEP2 MUTATED                                                    5
  DPEP2 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DPEP2 MUTATED                                            0
  DPEP2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DPEP2 MUTATED                                               1
  DPEP2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  DPEP2 MUTATED                                0
  DPEP2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  DPEP2 MUTATED                                    0
  DPEP2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DPEP2 MUTATED                              0                             0
  DPEP2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DPEP2 MUTATED                                               0
  DPEP2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  DPEP2 MUTATED                              0
  DPEP2 WILD-TYPE                            9
D292V9, multiclass
                                                    clus
vv                                                   DPEP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   DPEP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V10, binary
                 cls
clus                0   1
  DPEP2 MUTATED     0   7
  DPEP2 WILD-TYPE  20 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPEP2 MUTATED      0    7
  DPEP2 WILD-TYPE   20  453
     clus
vv    DPEP2 MUTATED DPEP2 WILD-TYPE
  NO              0              20
  YES             7             453
[1] 2 2
[1] FALSE
D292V11, continuous
D292V12, continuous
                 vv
clus               R0  R1  R2  RX
  DPEP2 MUTATED     6   0   0   1
  DPEP2 WILD-TYPE 304  11   4  24
D292V13, multiclass
    clus
vv   DPEP2 MUTATED DPEP2 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPEP2 MUTATED                                  0     0
  DPEP2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DPEP2 MUTATED                           0     6
  DPEP2 WILD-TYPE                        29   371
D292V14, multiclass
                                  clus
vv                                 DPEP2 MUTATED DPEP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V15, binary
                 cls
clus                0   1
  DPEP2 MUTATED     0   6
  DPEP2 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPEP2 MUTATED      0    6
  DPEP2 WILD-TYPE    6  343
                        clus
vv                       DPEP2 MUTATED DPEP2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(293) Variable = TCEAL5 MUTATION ANALYSIS
D293V1, survival
                  sevent
clus2                0   1
  TCEAL5 MUTATED    10   1
  TCEAL5 WILD-TYPE 305 140
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              11              445 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               1              140 
$`TCEAL5 MUTATED`
TCGA-44-5644 TCGA-44-6144 TCGA-44-6776 TCGA-49-6767 TCGA-50-8457 TCGA-53-A4EZ 
       28.37        23.77        63.72        22.26        25.61         9.21 
TCGA-55-7574 TCGA-55-8507 TCGA-73-4662 TCGA-86-8073 TCGA-MP-A4T4 
        3.12         0.26        29.98        24.33        86.04 

$`TCEAL5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       26.56        33.30        12.59        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        10.13         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       34.29        30.54        13.94        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
        7.04         2.01         0.10        52.60        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       58.45        49.35        37.35        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
            0.26             0.00 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           86.04           223.96 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           24.33            17.75 
[1] "0.3 - 86.0 (24.3)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "4.5"
D293V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TCEAL5 MUTATED         0        5        3         1         3          1
  TCEAL5 WILD-TYPE       4      118      130        45        64         69
                  vv
clus               STAGE IIIB STAGE IV
  TCEAL5 MUTATED            0        0
  TCEAL5 WILD-TYPE         11       25
D293V3, multiclass
            clus
vv           TCEAL5 MUTATED TCEAL5 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              118
  STAGE IB                3              130
  STAGE IIA               1               45
  STAGE IIB               3               64
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCEAL5 MUTATED     5   7   1   0
  TCEAL5 WILD-TYPE 150 254  42  18
D293V4, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  T1              5              150
  T2              7              254
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  TCEAL5 MUTATED     9   3     1
  TCEAL5 WILD-TYPE 298  86    71
D293V5, multiclass
       clus
vv      TCEAL5 MUTATED TCEAL5 WILD-TYPE
  N0                 9              298
  N1                 3               86
  N2+N3              1               71
[1] 3 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
  TCEAL5 MUTATED     8   0
  TCEAL5 WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      8    0
  TCEAL5 WILD-TYPE  319   23
   clus
vv  TCEAL5 MUTATED TCEAL5 WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D293V7, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     8   5
  TCEAL5 WILD-TYPE 251 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      8    5
  TCEAL5 WILD-TYPE  251  216
        clus
vv       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  FEMALE              8              251
  MALE                5              216
[1] 2 2
[1] FALSE
D293V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TCEAL5 MUTATED                            1                                 1
  TCEAL5 WILD-TYPE                         17                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TCEAL5 MUTATED                                                   10
  TCEAL5 WILD-TYPE                                                284
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TCEAL5 MUTATED                                            0
  TCEAL5 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TCEAL5 MUTATED                                               1
  TCEAL5 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TCEAL5 MUTATED                                0
  TCEAL5 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TCEAL5 MUTATED                                    0
  TCEAL5 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TCEAL5 MUTATED                              0                             0
  TCEAL5 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TCEAL5 MUTATED                                               0
  TCEAL5 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TCEAL5 MUTATED                              0
  TCEAL5 WILD-TYPE                            9
D293V9, multiclass
                                                    clus
vv                                                   TCEAL5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   TCEAL5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V10, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     1  12
  TCEAL5 WILD-TYPE  19 448
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      1   12
  TCEAL5 WILD-TYPE   19  448
     clus
vv    TCEAL5 MUTATED TCEAL5 WILD-TYPE
  NO               1               19
  YES             12              448
[1] 2 2
[1] FALSE
D293V11, continuous
D293V12, continuous
                  vv
clus                R0  R1  R2  RX
  TCEAL5 MUTATED     7   1   0   2
  TCEAL5 WILD-TYPE 303  10   4  23
D293V13, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  R0              7              303
  R1              1               10
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEAL5 MUTATED                                  0     0
  TCEAL5 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEAL5 MUTATED                           1    10
  TCEAL5 WILD-TYPE                        28   367
D293V14, multiclass
                                  clus
vv                                 TCEAL5 MUTATED TCEAL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V15, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     1   7
  TCEAL5 WILD-TYPE   5 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      1    7
  TCEAL5 WILD-TYPE    5  342
                        clus
vv                       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(294) Variable = PTPRH MUTATION ANALYSIS
D294V1, survival
                 sevent
clus2               0   1
  PTPRH MUTATED    15   6
  PTPRH WILD-TYPE 300 135
  PTPRH MUTATED PTPRH WILD-TYPE 
             21             435 
  PTPRH MUTATED PTPRH WILD-TYPE 
              6             135 
$`PTPRH MUTATED`
TCGA-05-4382 TCGA-05-4424 TCGA-44-4112 TCGA-44-8120 TCGA-49-4514 TCGA-53-7624 
       19.96        30.02        26.56         8.55        55.89        34.29 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7911 TCGA-55-8203 TCGA-55-8507 TCGA-55-8510 
        0.79         0.53        17.65        17.98         0.26        17.72 
TCGA-55-8616 TCGA-55-A490 TCGA-62-8398 TCGA-69-A59K TCGA-78-7148 TCGA-78-8662 
        1.58         1.58        14.60         7.04        20.58       110.50 
TCGA-93-8067 TCGA-MP-A4TC TCGA-MP-A4TH 
        6.12         2.43        14.66 

$`PTPRH WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24        34.06         6.25        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
       29.00        17.59        23.64        12.66         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 
       14.07        32.84         8.81        29.46        29.75        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7914 
        1.12         1.78         1.45        18.64         6.48         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
       19.73         5.06         0.13        23.64        15.65         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.36         0.49         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         0.49         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
        2.93        12.56        14.01        13.45         4.24         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        19.27        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       10.09        29.46        11.05        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  PTPRH MUTATED PTPRH WILD-TYPE 
           0.26            0.00 
  PTPRH MUTATED PTPRH WILD-TYPE 
         110.50          223.96 
  PTPRH MUTATED PTPRH WILD-TYPE 
          14.66           18.64 
[1] "0.3 - 110.5 (14.7)" "0.0 - 224.0 (18.6)"
[1] "hr=" "1.1"
D294V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PTPRH MUTATED         0        4       10         2         3          2
  PTPRH WILD-TYPE       4      119      123        44        64         68
                 vv
clus              STAGE IIIB STAGE IV
  PTPRH MUTATED            0        1
  PTPRH WILD-TYPE         11       24
D294V3, multiclass
            clus
vv           PTPRH MUTATED PTPRH WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB              10             123
  STAGE IIA              2              44
  STAGE IIB              3              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRH MUTATED     6  14   2   0
  PTPRH WILD-TYPE 149 247  41  18
D294V4, multiclass
    clus
vv   PTPRH MUTATED PTPRH WILD-TYPE
  T1             6             149
  T2            14             247
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PTPRH MUTATED    18   2     2
  PTPRH WILD-TYPE 289  87    70
D294V5, multiclass
       clus
vv      PTPRH MUTATED PTPRH WILD-TYPE
  N0               18             289
  N1                2              87
  N2+N3             2              70
[1] 3 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
  PTPRH MUTATED    13   1
  PTPRH WILD-TYPE 314  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRH MUTATED     13    1
  PTPRH WILD-TYPE  314   22
   clus
vv  PTPRH MUTATED PTPRH WILD-TYPE
  0            13             314
  1             1              22
[1] 2 2
[1] FALSE
D294V7, binary
                 cls
clus                0   1
  PTPRH MUTATED    11  11
  PTPRH WILD-TYPE 248 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRH MUTATED     11   11
  PTPRH WILD-TYPE  248  210
        clus
vv       PTPRH MUTATED PTPRH WILD-TYPE
  FEMALE            11             248
  MALE              11             210
[1] 2 2
[1] FALSE
D294V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PTPRH MUTATED                            0                                 5
  PTPRH WILD-TYPE                         18                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTPRH MUTATED                                                   15
  PTPRH WILD-TYPE                                                279
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PTPRH MUTATED                                            0
  PTPRH WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PTPRH MUTATED                                               0
  PTPRH WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PTPRH MUTATED                                0
  PTPRH WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PTPRH MUTATED                                    0
  PTPRH WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PTPRH MUTATED                              0                             1
  PTPRH WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PTPRH MUTATED                                               0
  PTPRH WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PTPRH MUTATED                              1
  PTPRH WILD-TYPE                            8
D294V9, multiclass
                                                    clus
vv                                                   PTPRH MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   PTPRH WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V10, binary
                 cls
clus                0   1
  PTPRH MUTATED     0  22
  PTPRH WILD-TYPE  20 438
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRH MUTATED      0   22
  PTPRH WILD-TYPE   20  438
     clus
vv    PTPRH MUTATED PTPRH WILD-TYPE
  NO              0              20
  YES            22             438
[1] 2 2
[1] FALSE
D294V11, continuous
D294V12, continuous
                 vv
clus               R0  R1  R2  RX
  PTPRH MUTATED    18   1   0   1
  PTPRH WILD-TYPE 292  10   4  24
D294V13, multiclass
    clus
vv   PTPRH MUTATED PTPRH WILD-TYPE
  R0            18             292
  R1             1              10
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRH MUTATED                                  0     1
  PTPRH WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRH MUTATED                           2    14
  PTPRH WILD-TYPE                        27   363
D294V14, multiclass
                                  clus
vv                                 PTPRH MUTATED PTPRH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V15, binary
                 cls
clus                0   1
  PTPRH MUTATED     1  14
  PTPRH WILD-TYPE   5 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRH MUTATED      1   14
  PTPRH WILD-TYPE    5  335
                        clus
vv                       PTPRH MUTATED PTPRH WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            14             335
[1] 2 2
[1] FALSE

Clustering(295) Variable = LMTK3 MUTATION ANALYSIS
D295V1, survival
                 sevent
clus2               0   1
  LMTK3 MUTATED     6   0
  LMTK3 WILD-TYPE 309 141
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              6             450 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              0             141 
$`LMTK3 MUTATED`
TCGA-44-3398 TCGA-55-7907 TCGA-55-8089 TCGA-55-A48Y TCGA-64-5781 TCGA-78-7160 
       38.24         0.53         3.29        20.71        51.25        22.29 

$`LMTK3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        22.65        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       64.90         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  LMTK3 MUTATED LMTK3 WILD-TYPE 
           0.53            0.00 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
          51.25          223.96 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
          21.50           17.95 
[1] "0.5 - 51.2 (21.5)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "9100000"
D295V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LMTK3 MUTATED         0        2        2         2         0          0
  LMTK3 WILD-TYPE       4      121      131        44        67         70
                 vv
clus              STAGE IIIB STAGE IV
  LMTK3 MUTATED            0        1
  LMTK3 WILD-TYPE         11       24
D295V3, multiclass
            clus
vv           LMTK3 MUTATED LMTK3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               2             131
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMTK3 MUTATED     2   4   0   1
  LMTK3 WILD-TYPE 153 257  43  17
D295V4, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  T1             2             153
  T2             4             257
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  LMTK3 MUTATED     5   1     1
  LMTK3 WILD-TYPE 302  88    71
D295V5, multiclass
       clus
vv      LMTK3 MUTATED LMTK3 WILD-TYPE
  N0                5             302
  N1                1              88
  N2+N3             1              71
[1] 3 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
  LMTK3 MUTATED     5   1
  LMTK3 WILD-TYPE 322  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      5    1
  LMTK3 WILD-TYPE  322   22
   clus
vv  LMTK3 MUTATED LMTK3 WILD-TYPE
  0             5             322
  1             1              22
[1] 2 2
[1] FALSE
D295V7, binary
                 cls
clus                0   1
  LMTK3 MUTATED     2   5
  LMTK3 WILD-TYPE 257 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      2    5
  LMTK3 WILD-TYPE  257  216
        clus
vv       LMTK3 MUTATED LMTK3 WILD-TYPE
  FEMALE             2             257
  MALE               5             216
[1] 2 2
[1] FALSE
D295V8, continuous
[1] "Remove cluster labels:" "LMTK3 MUTATED"         
clus
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" "LMTK3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LMTK3 MUTATED                            0                                 2
  LMTK3 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LMTK3 MUTATED                                                    4
  LMTK3 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LMTK3 MUTATED                                            0
  LMTK3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LMTK3 MUTATED                                               0
  LMTK3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  LMTK3 MUTATED                                0
  LMTK3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  LMTK3 MUTATED                                    0
  LMTK3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LMTK3 MUTATED                              0                             0
  LMTK3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LMTK3 MUTATED                                               1
  LMTK3 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  LMTK3 MUTATED                              0
  LMTK3 WILD-TYPE                            9
D295V9, multiclass
                                                    clus
vv                                                   LMTK3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   LMTK3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V10, binary
                 cls
clus                0   1
  LMTK3 MUTATED     0   7
  LMTK3 WILD-TYPE  20 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      0    7
  LMTK3 WILD-TYPE   20  453
     clus
vv    LMTK3 MUTATED LMTK3 WILD-TYPE
  NO              0              20
  YES             7             453
[1] 2 2
[1] FALSE
D295V11, continuous
D295V12, continuous
                 vv
clus               R0  R1  R2  RX
  LMTK3 MUTATED     7   0   0   0
  LMTK3 WILD-TYPE 303  11   4  25
D295V13, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LMTK3 MUTATED                                  0     0
  LMTK3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LMTK3 MUTATED                           0     6
  LMTK3 WILD-TYPE                        29   371
D295V14, multiclass
                                  clus
vv                                 LMTK3 MUTATED LMTK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V15, binary
                 cls
clus                0   1
  LMTK3 MUTATED     0   5
  LMTK3 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      0    5
  LMTK3 WILD-TYPE    6  344
                        clus
vv                       LMTK3 MUTATED LMTK3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(296) Variable = ADAR MUTATION ANALYSIS
D296V1, survival
                sevent
clus2              0   1
  ADAR MUTATED     6   3
  ADAR WILD-TYPE 309 138
  ADAR MUTATED ADAR WILD-TYPE 
             9            447 
  ADAR MUTATED ADAR WILD-TYPE 
             3            138 
$`ADAR MUTATED`
TCGA-05-4398 TCGA-38-4625 TCGA-53-7813 TCGA-55-6968 TCGA-55-8299 TCGA-55-A4DF 
       47.05        97.74        13.94        42.51        15.42        20.19 
TCGA-86-8671 TCGA-95-7567 TCGA-MN-A4N4 
       27.58        18.67        38.63 

$`ADAR WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       25.61         7.59        27.25        34.29        30.54         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        22.16         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       20.58        19.59         0.92        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
       19.00        17.29         1.12         1.22         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00        14.30         3.81         0.20        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ADAR MUTATED ADAR WILD-TYPE 
         13.94           0.00 
  ADAR MUTATED ADAR WILD-TYPE 
         97.74         223.96 
  ADAR MUTATED ADAR WILD-TYPE 
         27.58          17.75 
[1] "13.9 - 97.7 (27.6)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.5"
D296V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADAR MUTATED         0        3        1         0         2          0
  ADAR WILD-TYPE       4      120      132        46        65         70
                vv
clus             STAGE IIIB STAGE IV
  ADAR MUTATED            2        1
  ADAR WILD-TYPE          9       24
D296V3, multiclass
            clus
vv           ADAR MUTATED ADAR WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              1            132
  STAGE IIA             0             46
  STAGE IIB             2             65
  STAGE IIIA            0             70
  STAGE IIIB            2              9
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ADAR MUTATED     4   3   0   2
  ADAR WILD-TYPE 151 258  43  16
D296V4, multiclass
    clus
vv   ADAR MUTATED ADAR WILD-TYPE
  T1            4            151
  T2            3            258
  T3            0             43
  T4            2             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"
                vv
clus              N0  N1 N2+N3
  ADAR MUTATED     6   2     1
  ADAR WILD-TYPE 301  87    71
D296V5, multiclass
       clus
vv      ADAR MUTATED ADAR WILD-TYPE
  N0               6            301
  N1               2             87
  N2+N3            1             71
[1] 3 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
  ADAR MUTATED     6   1
  ADAR WILD-TYPE 321  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADAR MUTATED      6    1
  ADAR WILD-TYPE  321   22
   clus
vv  ADAR MUTATED ADAR WILD-TYPE
  0            6            321
  1            1             22
[1] 2 2
[1] FALSE
D296V7, binary
                cls
clus               0   1
  ADAR MUTATED     5   4
  ADAR WILD-TYPE 254 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADAR MUTATED      5    4
  ADAR WILD-TYPE  254  217
        clus
vv       ADAR MUTATED ADAR WILD-TYPE
  FEMALE            5            254
  MALE              4            217
[1] 2 2
[1] FALSE
D296V8, continuous
[1] "Remove cluster labels:" "ADAR MUTATED"          
clus
  ADAR MUTATED ADAR WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7711 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7954     TCGA-86-7955 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8074     TCGA-86-8075 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8281 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" "ADAR WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N5 
"ADAR WILD-TYPE" "ADAR WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADAR MUTATED                            0                                 2
  ADAR WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADAR MUTATED                                                    5
  ADAR WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADAR MUTATED                                            0
  ADAR WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADAR MUTATED                                               1
  ADAR WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  ADAR MUTATED                                0
  ADAR WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  ADAR MUTATED                                    0
  ADAR WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADAR MUTATED                              0                             1
  ADAR WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADAR MUTATED                                               0
  ADAR WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  ADAR MUTATED                              0
  ADAR WILD-TYPE                            9
D296V9, multiclass
                                                    clus
vv                                                   ADAR MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   ADAR WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V10, binary
                cls
clus               0   1
  ADAR MUTATED     0   9
  ADAR WILD-TYPE  20 451
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADAR MUTATED      0    9
  ADAR WILD-TYPE   20  451
     clus
vv    ADAR MUTATED ADAR WILD-TYPE
  NO             0             20
  YES            9            451
[1] 2 2
[1] FALSE
D296V11, continuous
D296V12, continuous
                vv
clus              R0  R1  R2  RX
  ADAR MUTATED     6   0   0   0
  ADAR WILD-TYPE 304  11   4  25
D296V13, multiclass
    clus
vv   ADAR MUTATED ADAR WILD-TYPE
  R0            6            304
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAR MUTATED                                  0     0
  ADAR WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ADAR MUTATED                           0     8
  ADAR WILD-TYPE                        29   369
D296V14, multiclass
                                  clus
vv                                 ADAR MUTATED ADAR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V15, binary
                cls
clus               0   1
  ADAR MUTATED     0   8
  ADAR WILD-TYPE   6 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADAR MUTATED      0    8
  ADAR WILD-TYPE    6  341
                        clus
vv                       ADAR MUTATED ADAR WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(297) Variable = CLCN5 MUTATION ANALYSIS
D297V1, survival
                 sevent
clus2               0   1
  CLCN5 MUTATED     9   0
  CLCN5 WILD-TYPE 306 141
  CLCN5 MUTATED CLCN5 WILD-TYPE 
              9             447 
  CLCN5 MUTATED CLCN5 WILD-TYPE 
              0             141 
$`CLCN5 MUTATED`
TCGA-38-4626 TCGA-55-6972 TCGA-55-7995 TCGA-55-8097 TCGA-69-7979 TCGA-78-7160 
      120.79        48.49         0.16        15.65         2.93        22.29 
TCGA-86-8358 TCGA-91-6849 TCGA-NJ-A55A 
       21.47         1.15         0.26 

$`CLCN5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15        19.82        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06         0.13        23.64        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.30        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       64.90         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.65        15.85        23.05        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  CLCN5 MUTATED CLCN5 WILD-TYPE 
           0.16            0.00 
  CLCN5 MUTATED CLCN5 WILD-TYPE 
         120.79          223.96 
  CLCN5 MUTATED CLCN5 WILD-TYPE 
          15.65           18.08 
[1] "0.2 - 120.8 (15.7)" "0.0 - 224.0 (18.1)"
[1] "hr="     "9600000"
D297V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CLCN5 MUTATED         0        2        4         1         0          1
  CLCN5 WILD-TYPE       4      121      129        45        67         69
                 vv
clus              STAGE IIIB STAGE IV
  CLCN5 MUTATED            0        1
  CLCN5 WILD-TYPE         11       24
D297V3, multiclass
            clus
vv           CLCN5 MUTATED CLCN5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLCN5 MUTATED     2   6   0   1
  CLCN5 WILD-TYPE 153 255  43  17
D297V4, multiclass
    clus
vv   CLCN5 MUTATED CLCN5 WILD-TYPE
  T1             2             153
  T2             6             255
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  CLCN5 MUTATED     7   0     2
  CLCN5 WILD-TYPE 300  89    70
D297V5, multiclass
       clus
vv      CLCN5 MUTATED CLCN5 WILD-TYPE
  N0                7             300
  N1                0              89
  N2+N3             2              70
[1] 3 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
  CLCN5 MUTATED     5   1
  CLCN5 WILD-TYPE 322  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN5 MUTATED      5    1
  CLCN5 WILD-TYPE  322   22
   clus
vv  CLCN5 MUTATED CLCN5 WILD-TYPE
  0             5             322
  1             1              22
[1] 2 2
[1] FALSE
D297V7, binary
                 cls
clus                0   1
  CLCN5 MUTATED     6   3
  CLCN5 WILD-TYPE 253 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN5 MUTATED      6    3
  CLCN5 WILD-TYPE  253  218
        clus
vv       CLCN5 MUTATED CLCN5 WILD-TYPE
  FEMALE             6             253
  MALE               3             218
[1] 2 2
[1] FALSE
D297V8, continuous
[1] "Remove cluster labels:" "CLCN5 MUTATED"         
clus
  CLCN5 MUTATED CLCN5 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-93-7348      TCGA-93-8067 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"CLCN5 WILD-TYPE" "CLCN5 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CLCN5 MUTATED                            1                                 1
  CLCN5 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CLCN5 MUTATED                                                    6
  CLCN5 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CLCN5 MUTATED                                            0
  CLCN5 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CLCN5 MUTATED                                               0
  CLCN5 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CLCN5 MUTATED                                0
  CLCN5 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CLCN5 MUTATED                                    0
  CLCN5 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CLCN5 MUTATED                              0                             1
  CLCN5 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CLCN5 MUTATED                                               0
  CLCN5 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CLCN5 MUTATED                              0
  CLCN5 WILD-TYPE                            9
D297V9, multiclass
                                                    clus
vv                                                   CLCN5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CLCN5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V10, binary
                 cls
clus                0   1
  CLCN5 MUTATED     0   9
  CLCN5 WILD-TYPE  20 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN5 MUTATED      0    9
  CLCN5 WILD-TYPE   20  451
     clus
vv    CLCN5 MUTATED CLCN5 WILD-TYPE
  NO              0              20
  YES             9             451
[1] 2 2
[1] FALSE
D297V11, continuous
D297V12, continuous
                 vv
clus               R0  R1  R2  RX
  CLCN5 MUTATED     6   0   0   0
  CLCN5 WILD-TYPE 304  11   4  25
D297V13, multiclass
    clus
vv   CLCN5 MUTATED CLCN5 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLCN5 MUTATED                                  0     0
  CLCN5 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLCN5 MUTATED                           1     8
  CLCN5 WILD-TYPE                        28   369
D297V14, multiclass
                                  clus
vv                                 CLCN5 MUTATED CLCN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V15, binary
                 cls
clus                0   1
  CLCN5 MUTATED     0   8
  CLCN5 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN5 MUTATED      0    8
  CLCN5 WILD-TYPE    6  341
                        clus
vv                       CLCN5 MUTATED CLCN5 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(298) Variable = MECP2 MUTATION ANALYSIS
D298V1, survival
                 sevent
clus2               0   1
  MECP2 MUTATED     6   3
  MECP2 WILD-TYPE 309 138
  MECP2 MUTATED MECP2 WILD-TYPE 
              9             447 
  MECP2 MUTATED MECP2 WILD-TYPE 
              3             138 
$`MECP2 MUTATED`
TCGA-05-4382 TCGA-44-A4SU TCGA-55-A4DF TCGA-73-4666 TCGA-78-7220 TCGA-91-6830 
       19.96        13.45        20.19        26.30        26.53         1.97 
TCGA-95-A4VN TCGA-99-7458 TCGA-J2-A4AE 
       18.18        24.56        35.47 

$`MECP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
        2.01         0.10        52.60        23.38        29.98        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        23.80        18.08        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MECP2 MUTATED MECP2 WILD-TYPE 
           1.97            0.00 
  MECP2 MUTATED MECP2 WILD-TYPE 
          35.47          223.96 
  MECP2 MUTATED MECP2 WILD-TYPE 
          20.19           17.75 
[1] "2.0 - 35.5 (20.2)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.4"
D298V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MECP2 MUTATED         0        3        1         2         0          2
  MECP2 WILD-TYPE       4      120      132        44        67         68
                 vv
clus              STAGE IIIB STAGE IV
  MECP2 MUTATED            0        1
  MECP2 WILD-TYPE         11       24
D298V3, multiclass
            clus
vv           MECP2 MUTATED MECP2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               1             132
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MECP2 MUTATED     5   3   0   1
  MECP2 WILD-TYPE 150 258  43  17
D298V4, multiclass
    clus
vv   MECP2 MUTATED MECP2 WILD-TYPE
  T1             5             150
  T2             3             258
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  MECP2 MUTATED     6   2     1
  MECP2 WILD-TYPE 301  87    71
D298V5, multiclass
       clus
vv      MECP2 MUTATED MECP2 WILD-TYPE
  N0                6             301
  N1                2              87
  N2+N3             1              71
[1] 3 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
  MECP2 MUTATED     4   1
  MECP2 WILD-TYPE 323  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECP2 MUTATED      4    1
  MECP2 WILD-TYPE  323   22
   clus
vv  MECP2 MUTATED MECP2 WILD-TYPE
  0             4             323
  1             1              22
[1] 2 2
[1] FALSE
D298V7, binary
                 cls
clus                0   1
  MECP2 MUTATED     7   2
  MECP2 WILD-TYPE 252 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECP2 MUTATED      7    2
  MECP2 WILD-TYPE  252  219
        clus
vv       MECP2 MUTATED MECP2 WILD-TYPE
  FEMALE             7             252
  MALE               2             219
[1] 2 2
[1] FALSE
D298V8, continuous
[1] "Remove cluster labels:" "MECP2 MUTATED"         
clus
  MECP2 MUTATED MECP2 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4668 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-MN-A4N1 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"MECP2 WILD-TYPE" "MECP2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MECP2 MUTATED                            0                                 2
  MECP2 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MECP2 MUTATED                                                    5
  MECP2 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MECP2 MUTATED                                            0
  MECP2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MECP2 MUTATED                                               1
  MECP2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MECP2 MUTATED                                0
  MECP2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MECP2 MUTATED                                    0
  MECP2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MECP2 MUTATED                              0                             0
  MECP2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MECP2 MUTATED                                               1
  MECP2 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MECP2 MUTATED                              0
  MECP2 WILD-TYPE                            9
D298V9, multiclass
                                                    clus
vv                                                   MECP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MECP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V10, binary
                 cls
clus                0   1
  MECP2 MUTATED     2   7
  MECP2 WILD-TYPE  18 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECP2 MUTATED      2    7
  MECP2 WILD-TYPE   18  453
     clus
vv    MECP2 MUTATED MECP2 WILD-TYPE
  NO              2              18
  YES             7             453
[1] 2 2
[1] FALSE
D298V11, continuous
D298V12, continuous
                 vv
clus               R0  R1  R2  RX
  MECP2 MUTATED     8   0   0   0
  MECP2 WILD-TYPE 302  11   4  25
D298V13, multiclass
    clus
vv   MECP2 MUTATED MECP2 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MECP2 MUTATED                                  0     0
  MECP2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MECP2 MUTATED                           0     8
  MECP2 WILD-TYPE                        29   369
D298V14, multiclass
                                  clus
vv                                 MECP2 MUTATED MECP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V15, binary
                 cls
clus                0   1
  MECP2 MUTATED     0   7
  MECP2 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECP2 MUTATED      0    7
  MECP2 WILD-TYPE    6  342
                        clus
vv                       MECP2 MUTATED MECP2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(299) Variable = IL22RA2 MUTATION ANALYSIS
D299V1, survival
                   sevent
clus2                 0   1
  IL22RA2 MUTATED     3   3
  IL22RA2 WILD-TYPE 312 138
  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
                6               450 
  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
                3               138 
$`IL22RA2 MUTATED`
TCGA-05-4390 TCGA-50-6590 TCGA-78-7146 TCGA-95-7039 TCGA-95-7562 TCGA-MN-A4N4 
       37.02        42.35         5.69         1.12         2.86        38.63 

$`IL22RA2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       39.09        23.51       163.10        27.16        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.22        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
             1.12              0.00 
  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
            42.35            223.96 
  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
           21.355            18.030 
[1] "1.1 - 42.4 (21.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.7"
D299V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IL22RA2 MUTATED         0        1        2         1         1          1
  IL22RA2 WILD-TYPE       4      122      131        45        66         69
                   vv
clus                STAGE IIIB STAGE IV
  IL22RA2 MUTATED            0        0
  IL22RA2 WILD-TYPE         11       25
D299V3, multiclass
            clus
vv           IL22RA2 MUTATED IL22RA2 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 2               131
  STAGE IIA                1                45
  STAGE IIB                1                66
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IL22RA2 MUTATED     1   4   1   0
  IL22RA2 WILD-TYPE 154 257  42  18
D299V4, multiclass
    clus
vv   IL22RA2 MUTATED IL22RA2 WILD-TYPE
  T1               1               154
  T2               4               257
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  IL22RA2 MUTATED     4   1     1
  IL22RA2 WILD-TYPE 303  88    71
D299V5, multiclass
       clus
vv      IL22RA2 MUTATED IL22RA2 WILD-TYPE
  N0                  4               303
  N1                  1                88
  N2+N3               1                71
[1] 3 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
  IL22RA2 MUTATED     5   0
  IL22RA2 WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL22RA2 MUTATED      5    0
  IL22RA2 WILD-TYPE  322   23
   clus
vv  IL22RA2 MUTATED IL22RA2 WILD-TYPE
  0               5               322
  1               0                23
[1] 2 2
[1] FALSE
D299V7, binary
                   cls
clus                  0   1
  IL22RA2 MUTATED     4   2
  IL22RA2 WILD-TYPE 255 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL22RA2 MUTATED      4    2
  IL22RA2 WILD-TYPE  255  219
        clus
vv       IL22RA2 MUTATED IL22RA2 WILD-TYPE
  FEMALE               4               255
  MALE                 2               219
[1] 2 2
[1] FALSE
D299V8, continuous
[1] "Remove cluster labels:" "IL22RA2 MUTATED"       
clus
  IL22RA2 MUTATED IL22RA2 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-93-7348        TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
       TCGA-99-7458        TCGA-MN-A4N1        TCGA-MN-A4N5 
"IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" "IL22RA2 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  IL22RA2 MUTATED                            0
  IL22RA2 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  IL22RA2 MUTATED                                   3
  IL22RA2 WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IL22RA2 MUTATED                                                    3
  IL22RA2 WILD-TYPE                                                291
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IL22RA2 MUTATED                                            0
  IL22RA2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IL22RA2 MUTATED                                               0
  IL22RA2 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  IL22RA2 MUTATED                                0
  IL22RA2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  IL22RA2 MUTATED                                    0
  IL22RA2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  IL22RA2 MUTATED                              0                             0
  IL22RA2 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IL22RA2 MUTATED                                               0
  IL22RA2 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  IL22RA2 MUTATED                              0
  IL22RA2 WILD-TYPE                            9
D299V9, multiclass
                                                    clus
vv                                                   IL22RA2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   IL22RA2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V10, binary
                   cls
clus                  0   1
  IL22RA2 MUTATED     0   6
  IL22RA2 WILD-TYPE  20 454
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL22RA2 MUTATED      0    6
  IL22RA2 WILD-TYPE   20  454
     clus
vv    IL22RA2 MUTATED IL22RA2 WILD-TYPE
  NO                0                20
  YES               6               454
[1] 2 2
[1] FALSE
D299V11, continuous
D299V12, continuous
                   vv
clus                 R0  R1  R2  RX
  IL22RA2 MUTATED     3   0   0   1
  IL22RA2 WILD-TYPE 307  11   4  24
D299V13, multiclass
    clus
vv   IL22RA2 MUTATED IL22RA2 WILD-TYPE
  R0               3               307
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL22RA2 MUTATED                                  0     0
  IL22RA2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  IL22RA2 MUTATED                           1     4
  IL22RA2 WILD-TYPE                        28   373
D299V14, multiclass
                                  clus
vv                                 IL22RA2 MUTATED IL22RA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          4               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V15, binary
                   cls
clus                  0   1
  IL22RA2 MUTATED     0   4
  IL22RA2 WILD-TYPE   6 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL22RA2 MUTATED      0    4
  IL22RA2 WILD-TYPE    6  345
                        clus
vv                       IL22RA2 MUTATED IL22RA2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               4               345
[1] 2 2
[1] FALSE

Clustering(300) Variable = MYO1H MUTATION ANALYSIS
D300V1, survival
                 sevent
clus2               0   1
  MYO1H MUTATED     8   4
  MYO1H WILD-TYPE 307 137
  MYO1H MUTATED MYO1H WILD-TYPE 
             12             444 
  MYO1H MUTATED MYO1H WILD-TYPE 
              4             137 
$`MYO1H MUTATED`
TCGA-05-4249 TCGA-05-4395 TCGA-05-5425 TCGA-44-6777 TCGA-50-5936 TCGA-55-8089 
       50.07         0.00        29.00        32.45         8.45         3.29 
TCGA-55-A493 TCGA-69-7978 TCGA-73-4666 TCGA-78-7156 TCGA-78-8640 TCGA-91-6828 
        0.92         2.30        26.30        32.09       214.62        10.62 

$`MYO1H WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        3.98        19.96        14.01        45.01        37.02         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
       15.02         4.96        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
       21.47        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       19.59        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        10.55        32.68        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       13.32        13.32        17.62        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MYO1H MUTATED MYO1H WILD-TYPE 
           0.00            0.07 
  MYO1H MUTATED MYO1H WILD-TYPE 
         214.62          223.96 
  MYO1H MUTATED MYO1H WILD-TYPE 
          18.46           18.03 
[1] "0.0 - 214.6 (18.5)" "0.1 - 224.0 (18.0)"
[1] "hr=" "1.2"
D300V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MYO1H MUTATED         0        2        3         1         2          1
  MYO1H WILD-TYPE       4      121      130        45        65         69
                 vv
clus              STAGE IIIB STAGE IV
  MYO1H MUTATED            1        2
  MYO1H WILD-TYPE         10       23
D300V3, multiclass
            clus
vv           MYO1H MUTATED MYO1H WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               3             130
  STAGE IIA              1              45
  STAGE IIB              2              65
  STAGE IIIA             1              69
  STAGE IIIB             1              10
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYO1H MUTATED     4   6   0   2
  MYO1H WILD-TYPE 151 255  43  16
D300V4, multiclass
    clus
vv   MYO1H MUTATED MYO1H WILD-TYPE
  T1             4             151
  T2             6             255
  T3             0              43
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  MYO1H MUTATED     5   4     2
  MYO1H WILD-TYPE 302  85    70
D300V5, multiclass
       clus
vv      MYO1H MUTATED MYO1H WILD-TYPE
  N0                5             302
  N1                4              85
  N2+N3             2              70
[1] 3 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
  MYO1H MUTATED     8   2
  MYO1H WILD-TYPE 319  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1H MUTATED      8    2
  MYO1H WILD-TYPE  319   21
   clus
vv  MYO1H MUTATED MYO1H WILD-TYPE
  0             8             319
  1             2              21
[1] 2 2
[1] FALSE
D300V7, binary
                 cls
clus                0   1
  MYO1H MUTATED     3   9
  MYO1H WILD-TYPE 256 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1H MUTATED      3    9
  MYO1H WILD-TYPE  256  212
        clus
vv       MYO1H MUTATED MYO1H WILD-TYPE
  FEMALE             3             256
  MALE               9             212
[1] 2 2
[1] FALSE
D300V8, continuous
[1] "Remove cluster labels:" "MYO1H MUTATED"         
clus
  MYO1H MUTATED MYO1H WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4668      TCGA-73-4676 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"MYO1H WILD-TYPE" "MYO1H WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MYO1H MUTATED                            0                                 4
  MYO1H WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MYO1H MUTATED                                                    7
  MYO1H WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MYO1H MUTATED                                            0
  MYO1H WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MYO1H MUTATED                                               0
  MYO1H WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MYO1H MUTATED                                0
  MYO1H WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MYO1H MUTATED                                    0
  MYO1H WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MYO1H MUTATED                              0                             0
  MYO1H WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MYO1H MUTATED                                               0
  MYO1H WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MYO1H MUTATED                              1
  MYO1H WILD-TYPE                            8
D300V9, multiclass
                                                    clus
vv                                                   MYO1H MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   MYO1H WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V10, binary
                 cls
clus                0   1
  MYO1H MUTATED     2  10
  MYO1H WILD-TYPE  18 450
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1H MUTATED      2   10
  MYO1H WILD-TYPE   18  450
     clus
vv    MYO1H MUTATED MYO1H WILD-TYPE
  NO              2              18
  YES            10             450
[1] 2 2
[1] FALSE
D300V11, continuous
D300V12, continuous
                 vv
clus               R0  R1  R2  RX
  MYO1H MUTATED     9   0   0   0
  MYO1H WILD-TYPE 301  11   4  25
D300V13, multiclass
    clus
vv   MYO1H MUTATED MYO1H WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO1H MUTATED                                  0     0
  MYO1H WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO1H MUTATED                           0     8
  MYO1H WILD-TYPE                        29   369
D300V14, multiclass
                                  clus
vv                                 MYO1H MUTATED MYO1H WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V15, binary
                 cls
clus                0   1
  MYO1H MUTATED     0   6
  MYO1H WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1H MUTATED      0    6
  MYO1H WILD-TYPE    6  343
                        clus
vv                       MYO1H MUTATED MYO1H WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(301) Variable = SERGEF MUTATION ANALYSIS
D301V1, survival
                  sevent
clus2                0   1
  SERGEF MUTATED     8   1
  SERGEF WILD-TYPE 307 140
  SERGEF MUTATED SERGEF WILD-TYPE 
               9              447 
  SERGEF MUTATED SERGEF WILD-TYPE 
               1              140 
$`SERGEF MUTATED`
TCGA-44-8117 TCGA-55-7994 TCGA-55-8506 TCGA-55-8512 TCGA-55-A4DG TCGA-78-7161 
       12.66        19.82         0.36         0.10        19.99         7.07 
TCGA-78-7220 TCGA-86-A4JF TCGA-95-7947 
       26.53        17.62        15.68 

$`SERGEF WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.30         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       64.90        22.29       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SERGEF MUTATED SERGEF WILD-TYPE 
             0.1              0.0 
  SERGEF MUTATED SERGEF WILD-TYPE 
           26.53           223.96 
  SERGEF MUTATED SERGEF WILD-TYPE 
           15.68            18.12 
[1] "0.1 - 26.5 (15.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D301V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SERGEF MUTATED         0        2        1         0         4          1
  SERGEF WILD-TYPE       4      121      132        46        63         69
                  vv
clus               STAGE IIIB STAGE IV
  SERGEF MUTATED            0        1
  SERGEF WILD-TYPE         11       24
D301V3, multiclass
            clus
vv           SERGEF MUTATED SERGEF WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                1              132
  STAGE IIA               0               46
  STAGE IIB               4               63
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SERGEF MUTATED     3   2   4   0
  SERGEF WILD-TYPE 152 259  39  18
D301V4, multiclass
    clus
vv   SERGEF MUTATED SERGEF WILD-TYPE
  T1              3              152
  T2              2              259
  T3              4               39
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  SERGEF MUTATED     7   1     1
  SERGEF WILD-TYPE 300  88    71
D301V5, multiclass
       clus
vv      SERGEF MUTATED SERGEF WILD-TYPE
  N0                 7              300
  N1                 1               88
  N2+N3              1               71
[1] 3 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
  SERGEF MUTATED     5   1
  SERGEF WILD-TYPE 322  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SERGEF MUTATED      5    1
  SERGEF WILD-TYPE  322   22
   clus
vv  SERGEF MUTATED SERGEF WILD-TYPE
  0              5              322
  1              1               22
[1] 2 2
[1] FALSE
D301V7, binary
                  cls
clus                 0   1
  SERGEF MUTATED     4   5
  SERGEF WILD-TYPE 255 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SERGEF MUTATED      4    5
  SERGEF WILD-TYPE  255  216
        clus
vv       SERGEF MUTATED SERGEF WILD-TYPE
  FEMALE              4              255
  MALE                5              216
[1] 2 2
[1] FALSE
D301V8, continuous
[1] "Remove cluster labels:" "SERGEF MUTATED"        
clus
  SERGEF MUTATED SERGEF WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"SERGEF WILD-TYPE" "SERGEF WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SERGEF MUTATED                            0                                 3
  SERGEF WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SERGEF MUTATED                                                    5
  SERGEF WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SERGEF MUTATED                                            0
  SERGEF WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SERGEF MUTATED                                               1
  SERGEF WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SERGEF MUTATED                                0
  SERGEF WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SERGEF MUTATED                                    0
  SERGEF WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SERGEF MUTATED                              0                             0
  SERGEF WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SERGEF MUTATED                                               0
  SERGEF WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SERGEF MUTATED                              0
  SERGEF WILD-TYPE                            9
D301V9, multiclass
                                                    clus
vv                                                   SERGEF MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SERGEF WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V10, binary
                  cls
clus                 0   1
  SERGEF MUTATED     1   8
  SERGEF WILD-TYPE  19 452
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SERGEF MUTATED      1    8
  SERGEF WILD-TYPE   19  452
     clus
vv    SERGEF MUTATED SERGEF WILD-TYPE
  NO               1               19
  YES              8              452
[1] 2 2
[1] FALSE
D301V11, continuous
D301V12, continuous
                  vv
clus                R0  R1  R2  RX
  SERGEF MUTATED     7   1   0   0
  SERGEF WILD-TYPE 303  10   4  25
D301V13, multiclass
    clus
vv   SERGEF MUTATED SERGEF WILD-TYPE
  R0              7              303
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERGEF MUTATED                                  0     0
  SERGEF WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SERGEF MUTATED                           0     9
  SERGEF WILD-TYPE                        29   368
D301V14, multiclass
                                  clus
vv                                 SERGEF MUTATED SERGEF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V15, binary
                  cls
clus                 0   1
  SERGEF MUTATED     0   7
  SERGEF WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SERGEF MUTATED      0    7
  SERGEF WILD-TYPE    6  342
                        clus
vv                       SERGEF MUTATED SERGEF WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(302) Variable = TRIP13 MUTATION ANALYSIS
D302V1, survival
                  sevent
clus2                0   1
  TRIP13 MUTATED     7   3
  TRIP13 WILD-TYPE 308 138
  TRIP13 MUTATED TRIP13 WILD-TYPE 
              10              446 
  TRIP13 MUTATED TRIP13 WILD-TYPE 
               3              138 
$`TRIP13 MUTATED`
TCGA-44-6145 TCGA-44-7662 TCGA-49-4486 TCGA-50-5930 TCGA-55-7574 TCGA-55-8506 
       10.78         7.17        76.21         9.27         3.12         0.36 
TCGA-55-A490 TCGA-64-5781 TCGA-73-4658 TCGA-MN-A4N5 
        1.58        51.25        52.60         2.76 

$`TRIP13 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 
       26.56        33.30        28.37        12.59        23.77         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 
       61.28        16.44        14.60        19.46        12.03        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        42.90        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        7.04         2.01         0.10        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.30         3.81         0.20        27.19        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  TRIP13 MUTATED TRIP13 WILD-TYPE 
            0.36             0.00 
  TRIP13 MUTATED TRIP13 WILD-TYPE 
           76.21           223.96 
  TRIP13 MUTATED TRIP13 WILD-TYPE 
            8.22            18.15 
[1] "0.4 - 76.2 (8.2)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D302V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TRIP13 MUTATED         0        3        5         1         1          1
  TRIP13 WILD-TYPE       4      120      128        45        66         69
                  vv
clus               STAGE IIIB STAGE IV
  TRIP13 MUTATED            0        0
  TRIP13 WILD-TYPE         11       25
D302V3, multiclass
            clus
vv           TRIP13 MUTATED TRIP13 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                5              128
  STAGE IIA               1               45
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP13 MUTATED     3   7   1   0
  TRIP13 WILD-TYPE 152 254  42  18
D302V4, multiclass
    clus
vv   TRIP13 MUTATED TRIP13 WILD-TYPE
  T1              3              152
  T2              7              254
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  TRIP13 MUTATED    10   0     1
  TRIP13 WILD-TYPE 297  89    71
D302V5, multiclass
       clus
vv      TRIP13 MUTATED TRIP13 WILD-TYPE
  N0                10              297
  N1                 0               89
  N2+N3              1               71
[1] 3 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
  TRIP13 MUTATED     8   0
  TRIP13 WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP13 MUTATED      8    0
  TRIP13 WILD-TYPE  319   23
   clus
vv  TRIP13 MUTATED TRIP13 WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D302V7, binary
                  cls
clus                 0   1
  TRIP13 MUTATED     5   6
  TRIP13 WILD-TYPE 254 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP13 MUTATED      5    6
  TRIP13 WILD-TYPE  254  215
        clus
vv       TRIP13 MUTATED TRIP13 WILD-TYPE
  FEMALE              5              254
  MALE                6              215
[1] 2 2
[1] FALSE
D302V8, continuous
[1] "Remove cluster labels:" "TRIP13 MUTATED"        
clus
  TRIP13 MUTATED TRIP13 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4 
"TRIP13 WILD-TYPE" "TRIP13 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TRIP13 MUTATED                            0                                 3
  TRIP13 WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TRIP13 MUTATED                                                    8
  TRIP13 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TRIP13 MUTATED                                            0
  TRIP13 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TRIP13 MUTATED                                               0
  TRIP13 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TRIP13 MUTATED                                0
  TRIP13 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TRIP13 MUTATED                                    0
  TRIP13 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TRIP13 MUTATED                              0                             0
  TRIP13 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TRIP13 MUTATED                                               0
  TRIP13 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TRIP13 MUTATED                              0
  TRIP13 WILD-TYPE                            9
D302V9, multiclass
                                                    clus
vv                                                   TRIP13 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   TRIP13 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V10, binary
                  cls
clus                 0   1
  TRIP13 MUTATED     2   9
  TRIP13 WILD-TYPE  18 451
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP13 MUTATED      2    9
  TRIP13 WILD-TYPE   18  451
     clus
vv    TRIP13 MUTATED TRIP13 WILD-TYPE
  NO               2               18
  YES              9              451
[1] 2 2
[1] FALSE
D302V11, continuous
D302V12, continuous
                  vv
clus                R0  R1  R2  RX
  TRIP13 MUTATED     6   1   0   1
  TRIP13 WILD-TYPE 304  10   4  24
D302V13, multiclass
    clus
vv   TRIP13 MUTATED TRIP13 WILD-TYPE
  R0              6              304
  R1              1               10
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIP13 MUTATED                                  0     0
  TRIP13 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIP13 MUTATED                           0    10
  TRIP13 WILD-TYPE                        29   367
D302V14, multiclass
                                  clus
vv                                 TRIP13 MUTATED TRIP13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V15, binary
                  cls
clus                 0   1
  TRIP13 MUTATED     0  10
  TRIP13 WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP13 MUTATED      0   10
  TRIP13 WILD-TYPE    6  339
                        clus
vv                       TRIP13 MUTATED TRIP13 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(303) Variable = GPR174 MUTATION ANALYSIS
D303V1, survival
                  sevent
clus2                0   1
  GPR174 MUTATED    12   4
  GPR174 WILD-TYPE 303 137
  GPR174 MUTATED GPR174 WILD-TYPE 
              16              440 
  GPR174 MUTATED GPR174 WILD-TYPE 
               4              137 
$`GPR174 MUTATED`
TCGA-05-4405 TCGA-38-4626 TCGA-49-6743 TCGA-50-5931 TCGA-50-5946 TCGA-50-6597 
       20.05       120.79        12.13        14.27        22.55        41.69 
TCGA-55-7994 TCGA-55-8203 TCGA-55-8208 TCGA-55-8302 TCGA-55-8506 TCGA-55-A48X 
       19.82        17.98        22.16         0.76         0.36        22.65 
TCGA-91-6829 TCGA-91-7771 TCGA-95-7043 TCGA-MP-A4SV 
       41.36        16.18         1.22        86.14 

$`GPR174 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
        2.04         7.40         5.98         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        14.63        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.22         9.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
       15.65         1.08         1.51         2.17        15.42         1.45 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        16.93        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
       13.32        17.62        13.64        26.47        10.62         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  GPR174 MUTATED GPR174 WILD-TYPE 
            0.36             0.00 
  GPR174 MUTATED GPR174 WILD-TYPE 
          120.79           223.96 
  GPR174 MUTATED GPR174 WILD-TYPE 
          19.935           17.835 
[1] "0.4 - 120.8 (19.9)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.6"
D303V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GPR174 MUTATED         0        3        7         2         3          1
  GPR174 WILD-TYPE       4      120      126        44        64         69
                  vv
clus               STAGE IIIB STAGE IV
  GPR174 MUTATED            0        0
  GPR174 WILD-TYPE         11       25
D303V3, multiclass
            clus
vv           GPR174 MUTATED GPR174 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                7              126
  STAGE IIA               2               44
  STAGE IIB               3               64
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR174 MUTATED     6   7   3   0
  GPR174 WILD-TYPE 149 254  40  18
D303V4, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  T1              6              149
  T2              7              254
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  GPR174 MUTATED    14   1     1
  GPR174 WILD-TYPE 293  88    71
D303V5, multiclass
       clus
vv      GPR174 MUTATED GPR174 WILD-TYPE
  N0                14              293
  N1                 1               88
  N2+N3              1               71
[1] 3 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
  GPR174 MUTATED     7   0
  GPR174 WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      7    0
  GPR174 WILD-TYPE  320   23
   clus
vv  GPR174 MUTATED GPR174 WILD-TYPE
  0              7              320
  1              0               23
[1] 2 2
[1] FALSE
D303V7, binary
                  cls
clus                 0   1
  GPR174 MUTATED    10   6
  GPR174 WILD-TYPE 249 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED     10    6
  GPR174 WILD-TYPE  249  215
        clus
vv       GPR174 MUTATED GPR174 WILD-TYPE
  FEMALE             10              249
  MALE                6              215
[1] 2 2
[1] FALSE
D303V8, continuous
[1] "Remove cluster labels:" "GPR174 MUTATED"        
clus
  GPR174 MUTATED GPR174 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"GPR174 WILD-TYPE" "GPR174 WILD-TYPE" "GPR174 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GPR174 MUTATED                            0                                 3
  GPR174 WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GPR174 MUTATED                                                   11
  GPR174 WILD-TYPE                                                283
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GPR174 MUTATED                                            0
  GPR174 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GPR174 MUTATED                                               1
  GPR174 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  GPR174 MUTATED                                1
  GPR174 WILD-TYPE                              1
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  GPR174 MUTATED                                    0
  GPR174 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GPR174 MUTATED                              0                             0
  GPR174 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GPR174 MUTATED                                               0
  GPR174 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  GPR174 MUTATED                              0
  GPR174 WILD-TYPE                            9
D303V9, multiclass
                                                    clus
vv                                                   GPR174 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   GPR174 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V10, binary
                  cls
clus                 0   1
  GPR174 MUTATED     0  16
  GPR174 WILD-TYPE  20 444
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      0   16
  GPR174 WILD-TYPE   20  444
     clus
vv    GPR174 MUTATED GPR174 WILD-TYPE
  NO               0               20
  YES             16              444
[1] 2 2
[1] FALSE
D303V11, continuous
D303V12, continuous
                  vv
clus                R0  R1  R2  RX
  GPR174 MUTATED    12   0   0   0
  GPR174 WILD-TYPE 298  11   4  25
D303V13, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  R0             12              298
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR174 MUTATED                                  0     0
  GPR174 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR174 MUTATED                           0    14
  GPR174 WILD-TYPE                        29   363
D303V14, multiclass
                                  clus
vv                                 GPR174 MUTATED GPR174 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        14              363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V15, binary
                  cls
clus                 0   1
  GPR174 MUTATED     0  11
  GPR174 WILD-TYPE   6 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      0   11
  GPR174 WILD-TYPE    6  338
                        clus
vv                       GPR174 MUTATED GPR174 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(304) Variable = VARS MUTATION ANALYSIS
D304V1, survival
                sevent
clus2              0   1
  VARS MUTATED     3   6
  VARS WILD-TYPE 312 135
  VARS MUTATED VARS WILD-TYPE 
             9            447 
  VARS MUTATED VARS WILD-TYPE 
             6            135 
$`VARS MUTATED`
TCGA-05-4402 TCGA-44-A479 TCGA-49-4488 TCGA-49-4506 TCGA-50-5936 TCGA-62-8399 
        8.02        15.98        28.57        32.84         8.45        88.64 
TCGA-64-1679 TCGA-78-7155 TCGA-78-7537 
       55.43        38.50        53.33 

$`VARS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.11        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        14.07         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
       21.47        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 
       39.25        40.96        29.92        56.81        20.65        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  VARS MUTATED VARS WILD-TYPE 
          8.02           0.00 
  VARS MUTATED VARS WILD-TYPE 
         88.64         223.96 
  VARS MUTATED VARS WILD-TYPE 
         32.84          17.92 
[1] "8.0 - 88.6 (32.8)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.2"
D304V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  VARS MUTATED         0        1        3         0         1          3
  VARS WILD-TYPE       4      122      130        46        66         67
                vv
clus             STAGE IIIB STAGE IV
  VARS MUTATED            0        1
  VARS WILD-TYPE         11       24
D304V3, multiclass
            clus
vv           VARS MUTATED VARS WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            3             67
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VARS MUTATED     2   7   0   0
  VARS WILD-TYPE 153 254  43  18
D304V4, multiclass
    clus
vv   VARS MUTATED VARS WILD-TYPE
  T1            2            153
  T2            7            254
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  VARS MUTATED     4   1     3
  VARS WILD-TYPE 303  88    69
D304V5, multiclass
       clus
vv      VARS MUTATED VARS WILD-TYPE
  N0               4            303
  N1               1             88
  N2+N3            3             69
[1] 3 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
  VARS MUTATED     6   1
  VARS WILD-TYPE 321  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      6    1
  VARS WILD-TYPE  321   22
   clus
vv  VARS MUTATED VARS WILD-TYPE
  0            6            321
  1            1             22
[1] 2 2
[1] FALSE
D304V7, binary
                cls
clus               0   1
  VARS MUTATED     5   4
  VARS WILD-TYPE 254 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      5    4
  VARS WILD-TYPE  254  217
        clus
vv       VARS MUTATED VARS WILD-TYPE
  FEMALE            5            254
  MALE              4            217
[1] 2 2
[1] FALSE
D304V8, continuous
[1] "Remove cluster labels:" "VARS MUTATED"          
clus
  VARS MUTATED VARS WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8402     TCGA-62-A46O 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"VARS WILD-TYPE" "VARS WILD-TYPE" "VARS WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  VARS MUTATED                            0                                 2
  VARS WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  VARS MUTATED                                                    5
  VARS WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  VARS MUTATED                                            0
  VARS WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  VARS MUTATED                                               0
  VARS WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  VARS MUTATED                                0
  VARS WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  VARS MUTATED                                    0
  VARS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  VARS MUTATED                              0                             1
  VARS WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  VARS MUTATED                                               0
  VARS WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  VARS MUTATED                              1
  VARS WILD-TYPE                            8
D304V9, multiclass
                                                    clus
vv                                                   VARS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   VARS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V10, binary
                cls
clus               0   1
  VARS MUTATED     0   9
  VARS WILD-TYPE  20 451
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      0    9
  VARS WILD-TYPE   20  451
     clus
vv    VARS MUTATED VARS WILD-TYPE
  NO             0             20
  YES            9            451
[1] 2 2
[1] FALSE
D304V11, continuous
D304V12, continuous
                vv
clus              R0  R1  R2  RX
  VARS MUTATED     6   1   1   0
  VARS WILD-TYPE 304  10   3  25
D304V13, multiclass
    clus
vv   VARS MUTATED VARS WILD-TYPE
  R0            6            304
  R1            1             10
  R2            1              3
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VARS MUTATED                                  0     0
  VARS WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VARS MUTATED                           1     6
  VARS WILD-TYPE                        28   371
D304V14, multiclass
                                  clus
vv                                 VARS MUTATED VARS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       6            371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V15, binary
                cls
clus               0   1
  VARS MUTATED     0   6
  VARS WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  VARS MUTATED      0    6
  VARS WILD-TYPE    6  343
                        clus
vv                       VARS MUTATED VARS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(305) Variable = CSNK1E MUTATION ANALYSIS
D305V1, survival
                  sevent
clus2                0   1
  CSNK1E MUTATED     4   2
  CSNK1E WILD-TYPE 311 139
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               6              450 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               2              139 
$`CSNK1E MUTATED`
TCGA-44-3918 TCGA-55-8506 TCGA-73-4658 TCGA-86-6851 TCGA-95-7562 TCGA-95-7948 
       34.06         0.36        52.60         5.88         2.86        15.65 

$`CSNK1E WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        38.24         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        7.04         2.01         0.10        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
        1.22        18.67        12.39        15.68        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  CSNK1E MUTATED CSNK1E WILD-TYPE 
            0.36             0.00 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
           52.60           223.96 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
          10.765           18.100 
[1] "0.4 - 52.6 (10.8)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D305V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CSNK1E MUTATED         0        1        2         2         1          0
  CSNK1E WILD-TYPE       4      122      131        44        66         70
                  vv
clus               STAGE IIIB STAGE IV
  CSNK1E MUTATED            0        0
  CSNK1E WILD-TYPE         11       25
D305V3, multiclass
            clus
vv           CSNK1E MUTATED CSNK1E WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                2              131
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CSNK1E MUTATED     2   3   1   0
  CSNK1E WILD-TYPE 153 258  42  18
D305V4, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  T1              2              153
  T2              3              258
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  CSNK1E MUTATED     4   2     0
  CSNK1E WILD-TYPE 303  87    72
D305V5, multiclass
       clus
vv      CSNK1E MUTATED CSNK1E WILD-TYPE
  N0                 4              303
  N1                 2               87
  N2+N3              0               72
[1] 3 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
  CSNK1E MUTATED     5   0
  CSNK1E WILD-TYPE 322  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      5    0
  CSNK1E WILD-TYPE  322   23
   clus
vv  CSNK1E MUTATED CSNK1E WILD-TYPE
  0              5              322
  1              0               23
[1] 2 2
[1] FALSE
D305V7, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     5   1
  CSNK1E WILD-TYPE 254 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      5    1
  CSNK1E WILD-TYPE  254  220
        clus
vv       CSNK1E MUTATED CSNK1E WILD-TYPE
  FEMALE              5              254
  MALE                1              220
[1] 2 2
[1] FALSE
D305V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CSNK1E MUTATED                            0                                 2
  CSNK1E WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CSNK1E MUTATED                                                    4
  CSNK1E WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CSNK1E MUTATED                                            0
  CSNK1E WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CSNK1E MUTATED                                               0
  CSNK1E WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CSNK1E MUTATED                                0
  CSNK1E WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CSNK1E MUTATED                                    0
  CSNK1E WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CSNK1E MUTATED                              0                             0
  CSNK1E WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CSNK1E MUTATED                                               0
  CSNK1E WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CSNK1E MUTATED                              0
  CSNK1E WILD-TYPE                            9
D305V9, multiclass
                                                    clus
vv                                                   CSNK1E MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CSNK1E WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V10, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     0   6
  CSNK1E WILD-TYPE  20 454
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      0    6
  CSNK1E WILD-TYPE   20  454
     clus
vv    CSNK1E MUTATED CSNK1E WILD-TYPE
  NO               0               20
  YES              6              454
[1] 2 2
[1] FALSE
D305V11, continuous
D305V12, continuous
                  vv
clus                R0  R1  R2  RX
  CSNK1E MUTATED     4   0   0   1
  CSNK1E WILD-TYPE 306  11   4  24
D305V13, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK1E MUTATED                                  0     0
  CSNK1E WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CSNK1E MUTATED                           1     5
  CSNK1E WILD-TYPE                        28   372
D305V14, multiclass
                                  clus
vv                                 CSNK1E MUTATED CSNK1E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V15, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     0   6
  CSNK1E WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      0    6
  CSNK1E WILD-TYPE    6  343
                        clus
vv                       CSNK1E MUTATED CSNK1E WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              343
[1] 2 2
[1] FALSE

Clustering(306) Variable = ANKRD7 MUTATION ANALYSIS
D306V1, survival
                  sevent
clus2                0   1
  ANKRD7 MUTATED     4   6
  ANKRD7 WILD-TYPE 311 135
  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
              10              446 
  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
               6              135 
$`ANKRD7 MUTATED`
TCGA-05-4424 TCGA-44-3396 TCGA-44-8117 TCGA-50-6592 TCGA-50-6673 TCGA-62-A46S 
       30.02        37.15        12.66        25.55         0.72        54.35 
TCGA-73-4658 TCGA-73-4670 TCGA-78-7155 TCGA-91-6829 
       52.60         4.31        38.50        41.36 

$`ANKRD7 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        17.59        23.64         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
       25.12        22.55        42.35         3.91        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       47.80        19.53        56.71        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24         7.04         2.01         0.10        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       29.98        26.30        15.35         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
            0.72             0.00 
  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
           54.35           223.96 
  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
          33.585           17.835 
[1] "0.7 - 54.4 (33.6)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.4"
D306V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ANKRD7 MUTATED         1        0        6         0         1          1
  ANKRD7 WILD-TYPE       3      123      127        46        66         69
                  vv
clus               STAGE IIIB STAGE IV
  ANKRD7 MUTATED            0        1
  ANKRD7 WILD-TYPE         11       24
D306V3, multiclass
            clus
vv           ANKRD7 MUTATED ANKRD7 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                0              123
  STAGE IB                6              127
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANKRD7 MUTATED     1   8   1   0
  ANKRD7 WILD-TYPE 154 253  42  18
D306V4, multiclass
    clus
vv   ANKRD7 MUTATED ANKRD7 WILD-TYPE
  T1              1              154
  T2              8              253
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ANKRD7 MUTATED     9   0     1
  ANKRD7 WILD-TYPE 298  89    71
D306V5, multiclass
       clus
vv      ANKRD7 MUTATED ANKRD7 WILD-TYPE
  N0                 9              298
  N1                 0               89
  N2+N3              1               71
[1] 3 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
  ANKRD7 MUTATED     8   1
  ANKRD7 WILD-TYPE 319  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD7 MUTATED      8    1
  ANKRD7 WILD-TYPE  319   22
   clus
vv  ANKRD7 MUTATED ANKRD7 WILD-TYPE
  0              8              319
  1              1               22
[1] 2 2
[1] FALSE
D306V7, binary
                  cls
clus                 0   1
  ANKRD7 MUTATED     6   4
  ANKRD7 WILD-TYPE 253 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD7 MUTATED      6    4
  ANKRD7 WILD-TYPE  253  217
        clus
vv       ANKRD7 MUTATED ANKRD7 WILD-TYPE
  FEMALE              6              253
  MALE                4              217
[1] 2 2
[1] FALSE
D306V8, continuous
[1] "Remove cluster labels:" "ANKRD7 MUTATED"        
clus
  ANKRD7 MUTATED ANKRD7 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46U 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" "ANKRD7 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ANKRD7 MUTATED                            0                                 1
  ANKRD7 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ANKRD7 MUTATED                                                    7
  ANKRD7 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ANKRD7 MUTATED                                            0
  ANKRD7 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ANKRD7 MUTATED                                               1
  ANKRD7 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ANKRD7 MUTATED                                0
  ANKRD7 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ANKRD7 MUTATED                                    0
  ANKRD7 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ANKRD7 MUTATED                              0                             1
  ANKRD7 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ANKRD7 MUTATED                                               0
  ANKRD7 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ANKRD7 MUTATED                              0
  ANKRD7 WILD-TYPE                            9
D306V9, multiclass
                                                    clus
vv                                                   ANKRD7 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ANKRD7 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V10, binary
                  cls
clus                 0   1
  ANKRD7 MUTATED     0  10
  ANKRD7 WILD-TYPE  20 450
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD7 MUTATED      0   10
  ANKRD7 WILD-TYPE   20  450
     clus
vv    ANKRD7 MUTATED ANKRD7 WILD-TYPE
  NO               0               20
  YES             10              450
[1] 2 2
[1] FALSE
D306V11, continuous
D306V12, continuous
                  vv
clus                R0  R1  R2  RX
  ANKRD7 MUTATED     7   1   0   0
  ANKRD7 WILD-TYPE 303  10   4  25
D306V13, multiclass
    clus
vv   ANKRD7 MUTATED ANKRD7 WILD-TYPE
  R0              7              303
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD7 MUTATED                                  0     0
  ANKRD7 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANKRD7 MUTATED                           0     9
  ANKRD7 WILD-TYPE                        29   368
D306V14, multiclass
                                  clus
vv                                 ANKRD7 MUTATED ANKRD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V15, binary
                  cls
clus                 0   1
  ANKRD7 MUTATED     0   7
  ANKRD7 WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD7 MUTATED      0    7
  ANKRD7 WILD-TYPE    6  342
                        clus
vv                       ANKRD7 MUTATED ANKRD7 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(307) Variable = SLC34A1 MUTATION ANALYSIS
D307V1, survival
                   sevent
clus2                 0   1
  SLC34A1 MUTATED     7   1
  SLC34A1 WILD-TYPE 308 140
  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
                8               448 
  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
                1               140 
$`SLC34A1 MUTATED`
TCGA-44-7671 TCGA-55-8302 TCGA-55-8510 TCGA-78-7535 TCGA-86-8074 TCGA-95-7043 
       17.59         0.76        17.72        31.20         0.79         1.22 
TCGA-95-A4VN TCGA-97-7554 
       18.18        25.48 

$`SLC34A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        29.00        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.95         0.36         0.26         0.49 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
      223.96         8.48        88.14        26.53         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       16.70        24.49         4.08         4.57        24.33        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.12         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
             0.76              0.00 
  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
            31.20            223.96 
  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
           17.655            18.100 
[1] "0.8 - 31.2 (17.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D307V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC34A1 MUTATED         0        1        5         2         0          1
  SLC34A1 WILD-TYPE       4      122      128        44        67         69
                   vv
clus                STAGE IIIB STAGE IV
  SLC34A1 MUTATED            0        0
  SLC34A1 WILD-TYPE         11       25
D307V3, multiclass
            clus
vv           SLC34A1 MUTATED SLC34A1 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 5               128
  STAGE IIA                2                44
  STAGE IIB                0                67
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC34A1 MUTATED     2   7   0   0
  SLC34A1 WILD-TYPE 153 254  43  18
D307V4, multiclass
    clus
vv   SLC34A1 MUTATED SLC34A1 WILD-TYPE
  T1               2               153
  T2               7               254
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  SLC34A1 MUTATED     6   2     1
  SLC34A1 WILD-TYPE 301  87    71
D307V5, multiclass
       clus
vv      SLC34A1 MUTATED SLC34A1 WILD-TYPE
  N0                  6               301
  N1                  2                87
  N2+N3               1                71
[1] 3 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
  SLC34A1 MUTATED     6   0
  SLC34A1 WILD-TYPE 321  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A1 MUTATED      6    0
  SLC34A1 WILD-TYPE  321   23
   clus
vv  SLC34A1 MUTATED SLC34A1 WILD-TYPE
  0               6               321
  1               0                23
[1] 2 2
[1] FALSE
D307V7, binary
                   cls
clus                  0   1
  SLC34A1 MUTATED     6   3
  SLC34A1 WILD-TYPE 253 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A1 MUTATED      6    3
  SLC34A1 WILD-TYPE  253  218
        clus
vv       SLC34A1 MUTATED SLC34A1 WILD-TYPE
  FEMALE               6               253
  MALE                 3               218
[1] 2 2
[1] FALSE
D307V8, continuous
[1] "Remove cluster labels:" "SLC34A1 MUTATED"       
clus
  SLC34A1 MUTATED SLC34A1 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8075        TCGA-86-8076 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" "SLC34A1 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SLC34A1 MUTATED                            0
  SLC34A1 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC34A1 MUTATED                                   2
  SLC34A1 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC34A1 MUTATED                                                    5
  SLC34A1 WILD-TYPE                                                289
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC34A1 MUTATED                                            0
  SLC34A1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC34A1 MUTATED                                               0
  SLC34A1 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SLC34A1 MUTATED                                0
  SLC34A1 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC34A1 MUTATED                                    0
  SLC34A1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC34A1 MUTATED                              0                             1
  SLC34A1 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC34A1 MUTATED                                               1
  SLC34A1 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SLC34A1 MUTATED                              0
  SLC34A1 WILD-TYPE                            9
D307V9, multiclass
                                                    clus
vv                                                   SLC34A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   SLC34A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V10, binary
                   cls
clus                  0   1
  SLC34A1 MUTATED     0   9
  SLC34A1 WILD-TYPE  20 451
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A1 MUTATED      0    9
  SLC34A1 WILD-TYPE   20  451
     clus
vv    SLC34A1 MUTATED SLC34A1 WILD-TYPE
  NO                0                20
  YES               9               451
[1] 2 2
[1] FALSE
D307V11, continuous
D307V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC34A1 MUTATED     7   0   0   0
  SLC34A1 WILD-TYPE 303  11   4  25
D307V13, multiclass
    clus
vv   SLC34A1 MUTATED SLC34A1 WILD-TYPE
  R0               7               303
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC34A1 MUTATED                                  0     0
  SLC34A1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC34A1 MUTATED                           1     7
  SLC34A1 WILD-TYPE                        28   370
D307V14, multiclass
                                  clus
vv                                 SLC34A1 MUTATED SLC34A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          7               370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V15, binary
                   cls
clus                  0   1
  SLC34A1 MUTATED     0   6
  SLC34A1 WILD-TYPE   6 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A1 MUTATED      0    6
  SLC34A1 WILD-TYPE    6  343
                        clus
vv                       SLC34A1 MUTATED SLC34A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               6               343
[1] 2 2
[1] FALSE

Clustering(308) Variable = MSN MUTATION ANALYSIS
D308V1, survival
               sevent
clus2             0   1
  MSN MUTATED     6   2
  MSN WILD-TYPE 309 139
  MSN MUTATED MSN WILD-TYPE 
            8           448 
  MSN MUTATED MSN WILD-TYPE 
            2           139 
$`MSN MUTATED`
TCGA-50-6590 TCGA-55-7281 TCGA-55-8506 TCGA-69-7765 TCGA-69-7973 TCGA-78-7150 
       42.35         0.59         0.36         5.42         7.56        21.90 
TCGA-86-6851 TCGA-86-8358 
        5.88        21.47 

$`MSN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       15.12        18.64        29.03        25.12        22.55         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1.74         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       22.68        13.61         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
       27.16         5.69        19.27        20.58        35.93        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  MSN MUTATED MSN WILD-TYPE 
         0.36          0.00 
  MSN MUTATED MSN WILD-TYPE 
        42.35        223.96 
  MSN MUTATED MSN WILD-TYPE 
         6.72         18.10 
[1] "0.4 - 42.4 (6.7)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.5"
D308V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MSN MUTATED         0        1        3         1         2          0
  MSN WILD-TYPE       4      122      130        45        65         70
               vv
clus            STAGE IIIB STAGE IV
  MSN MUTATED            0        1
  MSN WILD-TYPE         11       24
D308V3, multiclass
            clus
vv           MSN MUTATED MSN WILD-TYPE
  STAGE I              0             4
  STAGE IA             1           122
  STAGE IB             3           130
  STAGE IIA            1            45
  STAGE IIB            2            65
  STAGE IIIA           0            70
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MSN MUTATED     2   4   1   1
  MSN WILD-TYPE 153 257  42  17
D308V4, multiclass
    clus
vv   MSN MUTATED MSN WILD-TYPE
  T1           2           153
  T2           4           257
  T3           1            42
  T4           1            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"
               vv
clus             N0  N1 N2+N3
  MSN MUTATED     6   2     0
  MSN WILD-TYPE 301  87    72
D308V5, multiclass
       clus
vv      MSN MUTATED MSN WILD-TYPE
  N0              6           301
  N1              2            87
  N2+N3           0            72
[1] 3 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
  MSN MUTATED     6   0
  MSN WILD-TYPE 321  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED      6    0
  MSN WILD-TYPE  321   23
   clus
vv  MSN MUTATED MSN WILD-TYPE
  0           6           321
  1           0            23
[1] 2 2
[1] FALSE
D308V7, binary
               cls
clus              0   1
  MSN MUTATED     5   3
  MSN WILD-TYPE 254 218
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED      5    3
  MSN WILD-TYPE  254  218
        clus
vv       MSN MUTATED MSN WILD-TYPE
  FEMALE           5           254
  MALE             3           218
[1] 2 2
[1] FALSE
D308V8, continuous
[1] "Remove cluster labels:" "MSN MUTATED"           
clus
  MSN MUTATED MSN WILD-TYPE 
            1            83 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-62-A470    TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-64-5778    TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-73-4659    TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4676 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-73-7498    TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-86-7711    TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-86-8055    TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-86-8278    TCGA-86-8279    TCGA-86-8281    TCGA-86-8359    TCGA-86-8668 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-86-8669    TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-MN-A4N1    TCGA-MN-A4N4    TCGA-MN-A4N5 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MSN MUTATED                            0                                 3
  MSN WILD-TYPE                         18                                99
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MSN MUTATED                                                    5
  MSN WILD-TYPE                                                289
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MSN MUTATED                                            0
  MSN WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MSN MUTATED                                               0
  MSN WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MSN MUTATED                                0
  MSN WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MSN MUTATED                                    0                            0
  MSN WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MSN MUTATED                               0
  MSN WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MSN MUTATED                                               0
  MSN WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MSN MUTATED                              0
  MSN WILD-TYPE                            9
D308V9, multiclass
                                                    clus
vv                                                   MSN MUTATED MSN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            3            99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           5           289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V10, binary
               cls
clus              0   1
  MSN MUTATED     0   8
  MSN WILD-TYPE  20 452
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED      0    8
  MSN WILD-TYPE   20  452
     clus
vv    MSN MUTATED MSN WILD-TYPE
  NO            0            20
  YES           8           452
[1] 2 2
[1] FALSE
D308V11, continuous
D308V12, continuous
               vv
clus             R0  R1  R2  RX
  MSN MUTATED     4   0   0   0
  MSN WILD-TYPE 306  11   4  25
D308V13, multiclass
    clus
vv   MSN MUTATED MSN WILD-TYPE
  R0           4           306
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSN MUTATED                                  0     0
  MSN WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MSN MUTATED                           1     7
  MSN WILD-TYPE                        28   370
D308V14, multiclass
                                  clus
vv                                 MSN MUTATED MSN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                      7           370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V15, binary
               cls
clus              0   1
  MSN MUTATED     0   6
  MSN WILD-TYPE   6 343
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED      0    6
  MSN WILD-TYPE    6  343
                        clus
vv                       MSN MUTATED MSN WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           6           343
[1] 2 2
[1] FALSE

Clustering(309) Variable = FXYD5 MUTATION ANALYSIS
D309V1, survival
                 sevent
clus2               0   1
  FXYD5 MUTATED     5   1
  FXYD5 WILD-TYPE 310 140
  FXYD5 MUTATED FXYD5 WILD-TYPE 
              6             450 
  FXYD5 MUTATED FXYD5 WILD-TYPE 
              1             140 
$`FXYD5 MUTATED`
TCGA-05-4250 TCGA-50-5946 TCGA-69-7765 TCGA-78-7633 TCGA-78-8655 TCGA-86-8073 
        3.98        22.55         5.42        32.68        77.59        24.33 

$`FXYD5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        10.75        39.35        10.55       214.62        39.75 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  FXYD5 MUTATED FXYD5 WILD-TYPE 
           3.98            0.00 
  FXYD5 MUTATED FXYD5 WILD-TYPE 
          77.59          223.96 
  FXYD5 MUTATED FXYD5 WILD-TYPE 
          23.44           17.95 
[1] "4.0 - 77.6 (23.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.3"
D309V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FXYD5 MUTATED         0        3        1         0         0          1
  FXYD5 WILD-TYPE       4      120      132        46        67         69
                 vv
clus              STAGE IIIB STAGE IV
  FXYD5 MUTATED            0        1
  FXYD5 WILD-TYPE         11       24
D309V3, multiclass
            clus
vv           FXYD5 MUTATED FXYD5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               1             132
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FXYD5 MUTATED     2   2   1   1
  FXYD5 WILD-TYPE 153 259  42  17
D309V4, multiclass
    clus
vv   FXYD5 MUTATED FXYD5 WILD-TYPE
  T1             2             153
  T2             2             259
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  FXYD5 MUTATED     5   1     0
  FXYD5 WILD-TYPE 302  88    72
D309V5, multiclass
       clus
vv      FXYD5 MUTATED FXYD5 WILD-TYPE
  N0                5             302
  N1                1              88
  N2+N3             0              72
[1] 3 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
  FXYD5 MUTATED     4   0
  FXYD5 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FXYD5 MUTATED      4    0
  FXYD5 WILD-TYPE  323   23
   clus
vv  FXYD5 MUTATED FXYD5 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D309V7, binary
                 cls
clus                0   1
  FXYD5 MUTATED     2   4
  FXYD5 WILD-TYPE 257 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FXYD5 MUTATED      2    4
  FXYD5 WILD-TYPE  257  217
        clus
vv       FXYD5 MUTATED FXYD5 WILD-TYPE
  FEMALE             2             257
  MALE               4             217
[1] 2 2
[1] FALSE
D309V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FXYD5 MUTATED                            0                                 4
  FXYD5 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FXYD5 MUTATED                                                    1
  FXYD5 WILD-TYPE                                                293
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FXYD5 MUTATED                                            0
  FXYD5 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FXYD5 MUTATED                                               1
  FXYD5 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FXYD5 MUTATED                                0
  FXYD5 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FXYD5 MUTATED                                    0
  FXYD5 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FXYD5 MUTATED                              0                             0
  FXYD5 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FXYD5 MUTATED                                               0
  FXYD5 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FXYD5 MUTATED                              0
  FXYD5 WILD-TYPE                            9
D309V9, multiclass
                                                    clus
vv                                                   FXYD5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FXYD5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V10, binary
                 cls
clus                0   1
  FXYD5 MUTATED     0   6
  FXYD5 WILD-TYPE  20 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FXYD5 MUTATED      0    6
  FXYD5 WILD-TYPE   20  454
     clus
vv    FXYD5 MUTATED FXYD5 WILD-TYPE
  NO              0              20
  YES             6             454
[1] 2 2
[1] FALSE
D309V11, continuous
D309V12, continuous
                 vv
clus               R0  R1  R2  RX
  FXYD5 MUTATED     3   0   1   0
  FXYD5 WILD-TYPE 307  11   3  25
D309V13, multiclass
    clus
vv   FXYD5 MUTATED FXYD5 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             1               3
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FXYD5 MUTATED                                  0     0
  FXYD5 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FXYD5 MUTATED                           1     3
  FXYD5 WILD-TYPE                        28   374
D309V14, multiclass
                                  clus
vv                                 FXYD5 MUTATED FXYD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        3             374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V15, binary
                 cls
clus                0   1
  FXYD5 MUTATED     0   2
  FXYD5 WILD-TYPE   6 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FXYD5 MUTATED      0    2
  FXYD5 WILD-TYPE    6  347
                        clus
vv                       FXYD5 MUTATED FXYD5 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2             347
[1] 2 2
[1] FALSE

Clustering(310) Variable = NXF5 MUTATION ANALYSIS
D310V1, survival
                sevent
clus2              0   1
  NXF5 MUTATED     9   4
  NXF5 WILD-TYPE 306 137
  NXF5 MUTATED NXF5 WILD-TYPE 
            13            443 
  NXF5 MUTATED NXF5 WILD-TYPE 
             4            137 
$`NXF5 MUTATED`
TCGA-38-4626 TCGA-38-A44F TCGA-44-3398 TCGA-44-7670 TCGA-49-4487 TCGA-49-4488 
      120.79         4.37        38.24        29.00        28.11        28.57 
TCGA-49-4505 TCGA-50-5946 TCGA-55-8203 TCGA-55-A494 TCGA-86-6851 TCGA-97-7938 
       14.07        22.55        17.98        15.81         5.88         0.59 
TCGA-99-8028 
       36.76 

$`NXF5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
       76.21        12.66        35.54        46.72        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59         0.92        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79        25.48         5.95         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  NXF5 MUTATED NXF5 WILD-TYPE 
          0.59           0.00 
  NXF5 MUTATED NXF5 WILD-TYPE 
        120.79         223.96 
  NXF5 MUTATED NXF5 WILD-TYPE 
         22.55          17.92 
[1] "0.6 - 120.8 (22.6)" "0.0 - 224.0 (17.9)"
[1] "hr=" "1.2"
D310V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NXF5 MUTATED         0        6        3         3         1          0
  NXF5 WILD-TYPE       4      117      130        43        66         70
                vv
clus             STAGE IIIB STAGE IV
  NXF5 MUTATED            0        0
  NXF5 WILD-TYPE         11       25
D310V3, multiclass
            clus
vv           NXF5 MUTATED NXF5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              3            130
  STAGE IIA             3             43
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NXF5 MUTATED     9   4   0   0
  NXF5 WILD-TYPE 146 257  43  18
D310V4, multiclass
    clus
vv   NXF5 MUTATED NXF5 WILD-TYPE
  T1            9            146
  T2            4            257
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  NXF5 MUTATED    10   3     0
  NXF5 WILD-TYPE 297  86    72
D310V5, multiclass
       clus
vv      NXF5 MUTATED NXF5 WILD-TYPE
  N0              10            297
  N1               3             86
  N2+N3            0             72
[1] 3 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
  NXF5 MUTATED     8   0
  NXF5 WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF5 MUTATED      8    0
  NXF5 WILD-TYPE  319   23
   clus
vv  NXF5 MUTATED NXF5 WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D310V7, binary
                cls
clus               0   1
  NXF5 MUTATED    11   2
  NXF5 WILD-TYPE 248 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF5 MUTATED     11    2
  NXF5 WILD-TYPE  248  219
        clus
vv       NXF5 MUTATED NXF5 WILD-TYPE
  FEMALE           11            248
  MALE              2            219
[1] 2 2
[1] FALSE
D310V8, continuous
[1] "Remove cluster labels:" "NXF5 MUTATED"          
clus
  NXF5 MUTATED NXF5 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-55-A490     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"NXF5 WILD-TYPE" "NXF5 WILD-TYPE" "NXF5 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NXF5 MUTATED                            0                                 3
  NXF5 WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NXF5 MUTATED                                                    9
  NXF5 WILD-TYPE                                                285
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NXF5 MUTATED                                            0
  NXF5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NXF5 MUTATED                                               1
  NXF5 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  NXF5 MUTATED                                0
  NXF5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  NXF5 MUTATED                                    0
  NXF5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NXF5 MUTATED                              0                             0
  NXF5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NXF5 MUTATED                                               0
  NXF5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  NXF5 MUTATED                              0
  NXF5 WILD-TYPE                            9
D310V9, multiclass
                                                    clus
vv                                                   NXF5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   NXF5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V10, binary
                cls
clus               0   1
  NXF5 MUTATED     0  13
  NXF5 WILD-TYPE  20 447
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF5 MUTATED      0   13
  NXF5 WILD-TYPE   20  447
     clus
vv    NXF5 MUTATED NXF5 WILD-TYPE
  NO             0             20
  YES           13            447
[1] 2 2
[1] FALSE
D310V11, continuous
D310V12, continuous
                vv
clus              R0  R1  R2  RX
  NXF5 MUTATED    10   0   0   0
  NXF5 WILD-TYPE 300  11   4  25
D310V13, multiclass
    clus
vv   NXF5 MUTATED NXF5 WILD-TYPE
  R0           10            300
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NXF5 MUTATED                                  0     0
  NXF5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NXF5 MUTATED                           1    12
  NXF5 WILD-TYPE                        28   365
D310V14, multiclass
                                  clus
vv                                 NXF5 MUTATED NXF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      12            365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V15, binary
                cls
clus               0   1
  NXF5 MUTATED     1  11
  NXF5 WILD-TYPE   5 338
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF5 MUTATED      1   11
  NXF5 WILD-TYPE    5  338
                        clus
vv                       NXF5 MUTATED NXF5 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           11            338
[1] 2 2
[1] FALSE

Clustering(311) Variable = CDK16 MUTATION ANALYSIS
D311V1, survival
                 sevent
clus2               0   1
  CDK16 MUTATED     5   0
  CDK16 WILD-TYPE 310 141
  CDK16 MUTATED CDK16 WILD-TYPE 
              5             451 
  CDK16 MUTATED CDK16 WILD-TYPE 
              0             141 
$`CDK16 MUTATED`
TCGA-44-A479 TCGA-86-A4JF TCGA-91-6848 TCGA-95-7947 TCGA-97-7546 
       15.98        17.62         7.36        15.68        31.69 

$`CDK16 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25         8.55        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23        27.68         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 
        1.12         1.22         2.86        18.67        12.39        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       27.29         2.76        21.40        18.18        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CDK16 MUTATED CDK16 WILD-TYPE 
           7.36            0.00 
  CDK16 MUTATED CDK16 WILD-TYPE 
          31.69          223.96 
  CDK16 MUTATED CDK16 WILD-TYPE 
          15.98           18.12 
[1] "7.4 - 31.7 (16.0)"  "0.0 - 224.0 (18.1)"
[1] "hr="     "3300000"
D311V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CDK16 MUTATED         0        2        1         0         1          1
  CDK16 WILD-TYPE       4      121      132        46        66         69
                 vv
clus              STAGE IIIB STAGE IV
  CDK16 MUTATED            0        0
  CDK16 WILD-TYPE         11       25
D311V3, multiclass
            clus
vv           CDK16 MUTATED CDK16 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               1             132
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK16 MUTATED     2   2   1   0
  CDK16 WILD-TYPE 153 259  42  18
D311V4, multiclass
    clus
vv   CDK16 MUTATED CDK16 WILD-TYPE
  T1             2             153
  T2             2             259
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  CDK16 MUTATED     4   0     1
  CDK16 WILD-TYPE 303  89    71
D311V5, multiclass
       clus
vv      CDK16 MUTATED CDK16 WILD-TYPE
  N0                4             303
  N1                0              89
  N2+N3             1              71
[1] 3 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
  CDK16 MUTATED     2   0
  CDK16 WILD-TYPE 325  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK16 MUTATED      2    0
  CDK16 WILD-TYPE  325   23
   clus
vv  CDK16 MUTATED CDK16 WILD-TYPE
  0             2             325
  1             0              23
[1] 2 2
[1] FALSE
D311V7, binary
                 cls
clus                0   1
  CDK16 MUTATED     2   3
  CDK16 WILD-TYPE 257 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK16 MUTATED      2    3
  CDK16 WILD-TYPE  257  218
        clus
vv       CDK16 MUTATED CDK16 WILD-TYPE
  FEMALE             2             257
  MALE               3             218
[1] 2 2
[1] FALSE
D311V8, continuous
[1] "Remove cluster labels:" "CDK16 MUTATED"         
clus
  CDK16 MUTATED CDK16 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"CDK16 WILD-TYPE" "CDK16 WILD-TYPE" "CDK16 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CDK16 MUTATED                            1                                 1
  CDK16 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDK16 MUTATED                                                    3
  CDK16 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CDK16 MUTATED                                            0
  CDK16 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CDK16 MUTATED                                               0
  CDK16 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CDK16 MUTATED                                0
  CDK16 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CDK16 MUTATED                                    0
  CDK16 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CDK16 MUTATED                              0                             0
  CDK16 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CDK16 MUTATED                                               0
  CDK16 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CDK16 MUTATED                              0
  CDK16 WILD-TYPE                            9
D311V9, multiclass
                                                    clus
vv                                                   CDK16 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CDK16 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V10, binary
                 cls
clus                0   1
  CDK16 MUTATED     0   5
  CDK16 WILD-TYPE  20 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK16 MUTATED      0    5
  CDK16 WILD-TYPE   20  455
     clus
vv    CDK16 MUTATED CDK16 WILD-TYPE
  NO              0              20
  YES             5             455
[1] 2 2
[1] FALSE
D311V11, continuous
D311V12, continuous
                 vv
clus               R0  R1  R2  RX
  CDK16 MUTATED     4   0   0   0
  CDK16 WILD-TYPE 306  11   4  25
D311V13, multiclass
    clus
vv   CDK16 MUTATED CDK16 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK16 MUTATED                                  0     0
  CDK16 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK16 MUTATED                           1     4
  CDK16 WILD-TYPE                        28   373
D311V14, multiclass
                                  clus
vv                                 CDK16 MUTATED CDK16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V15, binary
                 cls
clus                0   1
  CDK16 MUTATED     0   5
  CDK16 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK16 MUTATED      0    5
  CDK16 WILD-TYPE    6  344
                        clus
vv                       CDK16 MUTATED CDK16 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(312) Variable = COL19A1 MUTATION ANALYSIS
D312V1, survival
                   sevent
clus2                 0   1
  COL19A1 MUTATED    30   8
  COL19A1 WILD-TYPE 285 133
  COL19A1 MUTATED COL19A1 WILD-TYPE 
               38               418 
  COL19A1 MUTATED COL19A1 WILD-TYPE 
                8               133 
$`COL19A1 MUTATED`
TCGA-05-4390 TCGA-05-4427 TCGA-38-4625 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 
       37.02        26.01        97.74        29.00        23.64         3.25 
TCGA-49-6743 TCGA-50-5931 TCGA-50-6594 TCGA-55-7907 TCGA-55-8089 TCGA-55-8203 
       12.13        14.27        12.16         0.53         3.29        17.98 
TCGA-55-8514 TCGA-55-8620 TCGA-55-A490 TCGA-55-A4DG TCGA-62-8399 TCGA-64-1677 
        6.64         2.17         1.58        19.99        88.64        20.65 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-69-7980 TCGA-69-8253 TCGA-71-6725 
       42.90        51.25        28.47        12.56        14.01         2.01 
TCGA-78-7155 TCGA-78-7166 TCGA-78-7220 TCGA-86-6851 TCGA-86-7954 TCGA-91-6829 
       38.50         8.48        26.53         5.88        19.89        41.36 
TCGA-91-6830 TCGA-91-A4BC TCGA-97-8172 TCGA-99-8032 TCGA-MN-A4N1 TCGA-MN-A4N4 
        1.97         1.45        17.92         1.45        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4TC 
        2.76         2.43 

$`COL19A1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       17.59        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
        8.81        29.46        29.75        55.89        14.63        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.58         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       20.19         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       13.61        39.25        40.96        29.92        56.81        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 
       38.37        87.98         2.04        28.41        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-8520 TCGA-73-4658 
        2.93        13.45         4.24         7.04         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        7.07       104.19       223.96        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
       31.13        34.39        13.87        20.55        19.43        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        1.15        16.18        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
        5.95         0.59         0.72        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        34.85        36.76         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
        3.81         0.20        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  COL19A1 MUTATED COL19A1 WILD-TYPE 
             0.53              0.00 
  COL19A1 MUTATED COL19A1 WILD-TYPE 
            97.74            223.96 
  COL19A1 MUTATED COL19A1 WILD-TYPE 
           16.095            18.150 
[1] "0.5 - 97.7 (16.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D312V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL19A1 MUTATED         1        6       13         8         4          6
  COL19A1 WILD-TYPE       3      117      120        38        63         64
                   vv
clus                STAGE IIIB STAGE IV
  COL19A1 MUTATED            0        1
  COL19A1 WILD-TYPE         11       24
D312V3, multiclass
            clus
vv           COL19A1 MUTATED COL19A1 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 6               117
  STAGE IB                13               120
  STAGE IIA                8                38
  STAGE IIB                4                63
  STAGE IIIA               6                64
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL19A1 MUTATED    15  22   2   0
  COL19A1 WILD-TYPE 140 239  41  18
D312V4, multiclass
    clus
vv   COL19A1 MUTATED COL19A1 WILD-TYPE
  T1              15               140
  T2              22               239
  T3               2                41
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  COL19A1 MUTATED    23  10     6
  COL19A1 WILD-TYPE 284  79    66
D312V5, multiclass
       clus
vv      COL19A1 MUTATED COL19A1 WILD-TYPE
  N0                 23               284
  N1                 10                79
  N2+N3               6                66
[1] 3 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
  COL19A1 MUTATED    28   1
  COL19A1 WILD-TYPE 299  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL19A1 MUTATED     28    1
  COL19A1 WILD-TYPE  299   22
   clus
vv  COL19A1 MUTATED COL19A1 WILD-TYPE
  0              28               299
  1               1                22
[1] 2 2
[1] FALSE
D312V7, binary
                   cls
clus                  0   1
  COL19A1 MUTATED    21  18
  COL19A1 WILD-TYPE 238 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL19A1 MUTATED     21   18
  COL19A1 WILD-TYPE  238  203
        clus
vv       COL19A1 MUTATED COL19A1 WILD-TYPE
  FEMALE              21               238
  MALE                18               203
[1] 2 2
[1] FALSE
D312V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  COL19A1 MUTATED                            1
  COL19A1 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL19A1 MUTATED                                   7
  COL19A1 WILD-TYPE                                95
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL19A1 MUTATED                                                   25
  COL19A1 WILD-TYPE                                                269
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL19A1 MUTATED                                            0
  COL19A1 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL19A1 MUTATED                                               3
  COL19A1 WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  COL19A1 MUTATED                                1
  COL19A1 WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  COL19A1 MUTATED                                    0
  COL19A1 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL19A1 MUTATED                              0                             2
  COL19A1 WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL19A1 MUTATED                                               0
  COL19A1 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  COL19A1 MUTATED                              0
  COL19A1 WILD-TYPE                            9
D312V9, multiclass
                                                    clus
vv                                                   COL19A1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              25
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   COL19A1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               269
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V10, binary
                   cls
clus                  0   1
  COL19A1 MUTATED     2  37
  COL19A1 WILD-TYPE  18 423
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL19A1 MUTATED      2   37
  COL19A1 WILD-TYPE   18  423
     clus
vv    COL19A1 MUTATED COL19A1 WILD-TYPE
  NO                2                18
  YES              37               423
[1] 2 2
[1] FALSE
D312V11, continuous
D312V12, continuous
                   vv
clus                 R0  R1  R2  RX
  COL19A1 MUTATED    27   0   0   1
  COL19A1 WILD-TYPE 283  11   4  24
D312V13, multiclass
    clus
vv   COL19A1 MUTATED COL19A1 WILD-TYPE
  R0              27               283
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL19A1 MUTATED                                  0     1
  COL19A1 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COL19A1 MUTATED                           4    31
  COL19A1 WILD-TYPE                        25   346
D312V14, multiclass
                                  clus
vv                                 COL19A1 MUTATED COL19A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      4                25
  WHITE                                         31               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V15, binary
                   cls
clus                  0   1
  COL19A1 MUTATED     1  31
  COL19A1 WILD-TYPE   5 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL19A1 MUTATED      1   31
  COL19A1 WILD-TYPE    5  318
                        clus
vv                       COL19A1 MUTATED COL19A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              31               318
[1] 2 2
[1] FALSE

Clustering(313) Variable = PTPRN MUTATION ANALYSIS
D313V1, survival
                 sevent
clus2               0   1
  PTPRN MUTATED    16   2
  PTPRN WILD-TYPE 299 139
  PTPRN MUTATED PTPRN WILD-TYPE 
             18             438 
  PTPRN MUTATED PTPRN WILD-TYPE 
              2             139 
$`PTPRN MUTATED`
TCGA-05-4424 TCGA-05-4427 TCGA-44-6775 TCGA-44-7659 TCGA-49-6767 TCGA-55-7907 
       30.02        26.01        23.18        14.60        22.26         0.53 
TCGA-55-A490 TCGA-55-A491 TCGA-64-5779 TCGA-69-7973 TCGA-69-7980 TCGA-78-7148 
        1.58        20.58        28.41         7.56        12.56        20.58 
TCGA-78-7155 TCGA-86-A4JF TCGA-91-7771 TCGA-95-7043 TCGA-NJ-A4YF TCGA-NJ-A55A 
       38.50        17.62        16.18         1.22        71.05         0.26 

$`PTPRN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        63.72        32.45        61.28        16.44 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       14.63        12.13        29.26        17.16        11.64        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 TCGA-55-A493 
       16.93        22.65        20.71        21.40        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         6.05         2.30         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        19.27        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG 
       11.05        14.66        14.10        19.13        73.91        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64        29.13         0.43        19.82        59.11 

  PTPRN MUTATED PTPRN WILD-TYPE 
           0.26            0.00 
  PTPRN MUTATED PTPRN WILD-TYPE 
          71.05          223.96 
  PTPRN MUTATED PTPRN WILD-TYPE 
          19.10           18.03 
[1] "0.3 - 71.0 (19.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "2.2"
D313V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PTPRN MUTATED         1        4        4         2         6          1
  PTPRN WILD-TYPE       3      119      129        44        61         69
                 vv
clus              STAGE IIIB STAGE IV
  PTPRN MUTATED            0        0
  PTPRN WILD-TYPE         11       25
D313V3, multiclass
            clus
vv           PTPRN MUTATED PTPRN WILD-TYPE
  STAGE I                1               3
  STAGE IA               4             119
  STAGE IB               4             129
  STAGE IIA              2              44
  STAGE IIB              6              61
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRN MUTATED     5   9   4   0
  PTPRN WILD-TYPE 150 252  39  18
D313V4, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  T1             5             150
  T2             9             252
  T3             4              39
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PTPRN MUTATED    14   3     1
  PTPRN WILD-TYPE 293  86    71
D313V5, multiclass
       clus
vv      PTPRN MUTATED PTPRN WILD-TYPE
  N0               14             293
  N1                3              86
  N2+N3             1              71
[1] 3 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
  PTPRN MUTATED    10   0
  PTPRN WILD-TYPE 317  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED     10    0
  PTPRN WILD-TYPE  317   23
   clus
vv  PTPRN MUTATED PTPRN WILD-TYPE
  0            10             317
  1             0              23
[1] 2 2
[1] FALSE
D313V7, binary
                 cls
clus                0   1
  PTPRN MUTATED     9   9
  PTPRN WILD-TYPE 250 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED      9    9
  PTPRN WILD-TYPE  250  212
        clus
vv       PTPRN MUTATED PTPRN WILD-TYPE
  FEMALE             9             250
  MALE               9             212
[1] 2 2
[1] FALSE
D313V8, continuous
[1] "Remove cluster labels:" "PTPRN MUTATED"         
clus
  PTPRN MUTATED PTPRN WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"PTPRN WILD-TYPE" "PTPRN WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PTPRN MUTATED                            1                                 6
  PTPRN WILD-TYPE                         17                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTPRN MUTATED                                                   11
  PTPRN WILD-TYPE                                                283
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PTPRN MUTATED                                            0
  PTPRN WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PTPRN MUTATED                                               0
  PTPRN WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PTPRN MUTATED                                0
  PTPRN WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PTPRN MUTATED                                    0
  PTPRN WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PTPRN MUTATED                              0                             0
  PTPRN WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PTPRN MUTATED                                               0
  PTPRN WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PTPRN MUTATED                              0
  PTPRN WILD-TYPE                            9
D313V9, multiclass
                                                    clus
vv                                                   PTPRN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PTPRN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V10, binary
                 cls
clus                0   1
  PTPRN MUTATED     1  17
  PTPRN WILD-TYPE  19 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED      1   17
  PTPRN WILD-TYPE   19  443
     clus
vv    PTPRN MUTATED PTPRN WILD-TYPE
  NO              1              19
  YES            17             443
[1] 2 2
[1] FALSE
D313V11, continuous
D313V12, continuous
                 vv
clus               R0  R1  R2  RX
  PTPRN MUTATED     9   1   0   1
  PTPRN WILD-TYPE 301  10   4  24
D313V13, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  R0             9             301
  R1             1              10
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRN MUTATED                                  0     0
  PTPRN WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRN MUTATED                           1    15
  PTPRN WILD-TYPE                        28   362
D313V14, multiclass
                                  clus
vv                                 PTPRN MUTATED PTPRN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       15             362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V15, binary
                 cls
clus                0   1
  PTPRN MUTATED     1  12
  PTPRN WILD-TYPE   5 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED      1   12
  PTPRN WILD-TYPE    5  337
                        clus
vv                       PTPRN MUTATED PTPRN WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(314) Variable = FBXW7 MUTATION ANALYSIS
D314V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    10   2
  FBXW7 WILD-TYPE 305 139
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             12             444 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2             139 
$`FBXW7 MUTATED`
TCGA-05-4398 TCGA-38-7271 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 
       47.05        26.30        18.64         0.53         6.15         0.16 
TCGA-55-8089 TCGA-55-A490 TCGA-86-8073 TCGA-86-8358 TCGA-95-7039 TCGA-NJ-A4YP 
        3.29         1.58        24.33        21.47         1.12         1.64 

$`FBXW7 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 
        1.78         1.45         6.48        17.65        19.82        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        6.12        23.61         1.08        19.00        17.29         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13        29.13         0.26         0.43        19.82        59.11 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.16            0.00 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          47.05          223.96 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
           4.72           18.10 
[1] "0.2 - 47.0 (4.7)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D314V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FBXW7 MUTATED         0        4        3         3         1          0
  FBXW7 WILD-TYPE       4      119      130        43        66         70
                 vv
clus              STAGE IIIB STAGE IV
  FBXW7 MUTATED            1        0
  FBXW7 WILD-TYPE         10       25
D314V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               3             130
  STAGE IIA              3              43
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of 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     5   5   1   1
  FBXW7 WILD-TYPE 150 256  42  17
D314V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             5             150
  T2             5             256
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  FBXW7 MUTATED     9   2     1
  FBXW7 WILD-TYPE 298  87    71
D314V5, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  N0                9             298
  N1                2              87
  N2+N3             1              71
[1] 3 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
  FBXW7 MUTATED     7   0
  FBXW7 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      7    0
  FBXW7 WILD-TYPE  320   23
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0             7             320
  1             0              23
[1] 2 2
[1] FALSE
D314V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED     5   7
  FBXW7 WILD-TYPE 254 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      5    7
  FBXW7 WILD-TYPE  254  214
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             5             254
  MALE               7             214
[1] 2 2
[1] FALSE
D314V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FBXW7 MUTATED                            0                                 2
  FBXW7 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                    8
  FBXW7 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FBXW7 MUTATED                                            0
  FBXW7 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FBXW7 MUTATED                                               1
  FBXW7 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FBXW7 MUTATED                                0
  FBXW7 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FBXW7 MUTATED                                    0
  FBXW7 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FBXW7 MUTATED                              0                             1
  FBXW7 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FBXW7 MUTATED                                               0
  FBXW7 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FBXW7 MUTATED                              0
  FBXW7 WILD-TYPE                            9
D314V9, multiclass
                                                    clus
vv                                                   FBXW7 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FBXW7 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V10, binary
                 cls
clus                0   1
  FBXW7 MUTATED     0  12
  FBXW7 WILD-TYPE  20 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0   12
  FBXW7 WILD-TYPE   20  448
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              0              20
  YES            12             448
[1] 2 2
[1] FALSE
D314V11, continuous
D314V12, continuous
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    10   0   0   0
  FBXW7 WILD-TYPE 300  11   4  25
D314V13, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            10             300
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  0     0
  FBXW7 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED                           0    11
  FBXW7 WILD-TYPE                        29   366
D314V14, multiclass
                                  clus
vv                                 FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V15, binary
                 cls
clus                0   1
  FBXW7 MUTATED     0  11
  FBXW7 WILD-TYPE   6 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0   11
  FBXW7 WILD-TYPE    6  338
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            11             338
[1] 2 2
[1] FALSE

Clustering(315) Variable = SYTL1 MUTATION ANALYSIS
D315V1, survival
                 sevent
clus2               0   1
  SYTL1 MUTATED     4   1
  SYTL1 WILD-TYPE 311 140
  SYTL1 MUTATED SYTL1 WILD-TYPE 
              5             451 
  SYTL1 MUTATED SYTL1 WILD-TYPE 
              1             140 
$`SYTL1 MUTATED`
TCGA-05-4395 TCGA-86-8673 TCGA-93-8067 TCGA-95-7039 TCGA-MN-A4N4 
        0.00        14.96         6.12         1.12        38.63 

$`SYTL1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       30.84        27.58         0.62        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        9.76         4.18        23.61         1.08        19.00        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81         0.20        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SYTL1 MUTATED SYTL1 WILD-TYPE 
           0.00            0.07 
  SYTL1 MUTATED SYTL1 WILD-TYPE 
          38.63          223.96 
  SYTL1 MUTATED SYTL1 WILD-TYPE 
           6.12           18.12 
[1] "0.0 - 38.6 (6.1)"   "0.1 - 224.0 (18.1)"
[1] "hr=" "1.3"
D315V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SYTL1 MUTATED         0        1        2         0         1          0
  SYTL1 WILD-TYPE       4      122      131        46        66         70
                 vv
clus              STAGE IIIB STAGE IV
  SYTL1 MUTATED            1        0
  SYTL1 WILD-TYPE         10       25
D315V3, multiclass
            clus
vv           SYTL1 MUTATED SYTL1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               2             131
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYTL1 MUTATED     1   2   1   1
  SYTL1 WILD-TYPE 154 259  42  17
D315V4, multiclass
    clus
vv   SYTL1 MUTATED SYTL1 WILD-TYPE
  T1             1             154
  T2             2             259
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  SYTL1 MUTATED     4   0     1
  SYTL1 WILD-TYPE 303  89    71
D315V5, multiclass
       clus
vv      SYTL1 MUTATED SYTL1 WILD-TYPE
  N0                4             303
  N1                0              89
  N2+N3             1              71
[1] 3 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
  SYTL1 MUTATED     3   0
  SYTL1 WILD-TYPE 324  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYTL1 MUTATED      3    0
  SYTL1 WILD-TYPE  324   23
   clus
vv  SYTL1 MUTATED SYTL1 WILD-TYPE
  0             3             324
  1             0              23
[1] 2 2
[1] FALSE
D315V7, binary
                 cls
clus                0   1
  SYTL1 MUTATED     1   4
  SYTL1 WILD-TYPE 258 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYTL1 MUTATED      1    4
  SYTL1 WILD-TYPE  258  217
        clus
vv       SYTL1 MUTATED SYTL1 WILD-TYPE
  FEMALE             1             258
  MALE               4             217
[1] 2 2
[1] FALSE
D315V8, continuous
[1] "Remove cluster labels:" "SYTL1 MUTATED"         
clus
  SYTL1 MUTATED SYTL1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N5 
"SYTL1 WILD-TYPE" "SYTL1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SYTL1 MUTATED                            0                                 2
  SYTL1 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SYTL1 MUTATED                                                    2
  SYTL1 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SYTL1 MUTATED                                            0
  SYTL1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SYTL1 MUTATED                                               1
  SYTL1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SYTL1 MUTATED                                0
  SYTL1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SYTL1 MUTATED                                    0
  SYTL1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SYTL1 MUTATED                              0                             0
  SYTL1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SYTL1 MUTATED                                               0
  SYTL1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SYTL1 MUTATED                              0
  SYTL1 WILD-TYPE                            9
D315V9, multiclass
                                                    clus
vv                                                   SYTL1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SYTL1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V10, binary
                 cls
clus                0   1
  SYTL1 MUTATED     0   5
  SYTL1 WILD-TYPE  20 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYTL1 MUTATED      0    5
  SYTL1 WILD-TYPE   20  455
     clus
vv    SYTL1 MUTATED SYTL1 WILD-TYPE
  NO              0              20
  YES             5             455
[1] 2 2
[1] FALSE
D315V11, continuous
D315V12, continuous
                 vv
clus               R0  R1  R2  RX
  SYTL1 MUTATED     3   0   0   1
  SYTL1 WILD-TYPE 307  11   4  24
D315V13, multiclass
    clus
vv   SYTL1 MUTATED SYTL1 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYTL1 MUTATED                                  0     1
  SYTL1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYTL1 MUTATED                           0     3
  SYTL1 WILD-TYPE                        29   374
D315V14, multiclass
                                  clus
vv                                 SYTL1 MUTATED SYTL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        3             374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V15, binary
                 cls
clus                0   1
  SYTL1 MUTATED     0   4
  SYTL1 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYTL1 MUTATED      0    4
  SYTL1 WILD-TYPE    6  345
                        clus
vv                       SYTL1 MUTATED SYTL1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(316) Variable = PIK3C2B MUTATION ANALYSIS
D316V1, survival
                   sevent
clus2                 0   1
  PIK3C2B MUTATED    13   6
  PIK3C2B WILD-TYPE 302 135
  PIK3C2B MUTATED PIK3C2B WILD-TYPE 
               19               437 
  PIK3C2B MUTATED PIK3C2B WILD-TYPE 
                6               135 
$`PIK3C2B MUTATED`
TCGA-05-4250 TCGA-49-4505 TCGA-55-6971 TCGA-55-7994 TCGA-55-8091 TCGA-55-8506 
        3.98        14.07         0.82        19.82        19.73         0.36 
TCGA-69-7973 TCGA-71-6725 TCGA-78-7155 TCGA-86-6851 TCGA-86-7714 TCGA-86-8672 
        7.56         2.01        38.50         5.88        20.55         0.62 
TCGA-95-7567 TCGA-97-7547 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T4 
       18.67        64.60         0.20        38.63         2.76        86.04 
TCGA-NJ-A4YF 
       71.05 

$`PIK3C2B WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        46.72        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 
        0.79        42.51        40.73        15.25        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
        0.16        29.72        15.19         3.29        19.66         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24         7.04         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        13.87        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
        1.15        13.91        30.84        27.58        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.18        19.89        31.69        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30         3.81        27.19        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        19.13        73.91        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  PIK3C2B MUTATED PIK3C2B WILD-TYPE 
              0.2               0.0 
  PIK3C2B MUTATED PIK3C2B WILD-TYPE 
            86.04            223.96 
  PIK3C2B MUTATED PIK3C2B WILD-TYPE 
            14.07             18.08 
[1] "0.2 - 86.0 (14.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D316V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PIK3C2B MUTATED         0        4        6         1         6          2
  PIK3C2B WILD-TYPE       4      119      127        45        61         68
                   vv
clus                STAGE IIIB STAGE IV
  PIK3C2B MUTATED            0        0
  PIK3C2B WILD-TYPE         11       25
D316V3, multiclass
            clus
vv           PIK3C2B MUTATED PIK3C2B WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 4               119
  STAGE IB                 6               127
  STAGE IIA                1                45
  STAGE IIB                6                61
  STAGE IIIA               2                68
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3C2B MUTATED     6   9   4   0
  PIK3C2B WILD-TYPE 149 252  39  18
D316V4, multiclass
    clus
vv   PIK3C2B MUTATED PIK3C2B WILD-TYPE
  T1               6               149
  T2               9               252
  T3               4                39
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  PIK3C2B MUTATED    13   5     1
  PIK3C2B WILD-TYPE 294  84    71
D316V5, multiclass
       clus
vv      PIK3C2B MUTATED PIK3C2B WILD-TYPE
  N0                 13               294
  N1                  5                84
  N2+N3               1                71
[1] 3 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
  PIK3C2B MUTATED    13   0
  PIK3C2B WILD-TYPE 314  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2B MUTATED     13    0
  PIK3C2B WILD-TYPE  314   23
   clus
vv  PIK3C2B MUTATED PIK3C2B WILD-TYPE
  0              13               314
  1               0                23
[1] 2 2
[1] FALSE
D316V7, binary
                   cls
clus                  0   1
  PIK3C2B MUTATED    12   7
  PIK3C2B WILD-TYPE 247 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2B MUTATED     12    7
  PIK3C2B WILD-TYPE  247  214
        clus
vv       PIK3C2B MUTATED PIK3C2B WILD-TYPE
  FEMALE              12               247
  MALE                 7               214
[1] 2 2
[1] FALSE
D316V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PIK3C2B MUTATED                            0
  PIK3C2B WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PIK3C2B MUTATED                                   5
  PIK3C2B WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PIK3C2B MUTATED                                                   12
  PIK3C2B WILD-TYPE                                                282
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PIK3C2B MUTATED                                            0
  PIK3C2B WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PIK3C2B MUTATED                                               0
  PIK3C2B WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  PIK3C2B MUTATED                                0
  PIK3C2B WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  PIK3C2B MUTATED                                    0
  PIK3C2B WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PIK3C2B MUTATED                              0                             2
  PIK3C2B WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PIK3C2B MUTATED                                               0
  PIK3C2B WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  PIK3C2B MUTATED                              0
  PIK3C2B WILD-TYPE                            9
D316V9, multiclass
                                                    clus
vv                                                   PIK3C2B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   PIK3C2B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V10, binary
                   cls
clus                  0   1
  PIK3C2B MUTATED     0  19
  PIK3C2B WILD-TYPE  20 441
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2B MUTATED      0   19
  PIK3C2B WILD-TYPE   20  441
     clus
vv    PIK3C2B MUTATED PIK3C2B WILD-TYPE
  NO                0                20
  YES              19               441
[1] 2 2
[1] FALSE
D316V11, continuous
D316V12, continuous
                   vv
clus                 R0  R1  R2  RX
  PIK3C2B MUTATED    12   0   1   1
  PIK3C2B WILD-TYPE 298  11   3  24
D316V13, multiclass
    clus
vv   PIK3C2B MUTATED PIK3C2B WILD-TYPE
  R0              12               298
  R1               0                11
  R2               1                 3
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3C2B MUTATED                                  0     1
  PIK3C2B WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PIK3C2B MUTATED                           2    15
  PIK3C2B WILD-TYPE                        27   362
D316V14, multiclass
                                  clus
vv                                 PIK3C2B MUTATED PIK3C2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         15               362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V15, binary
                   cls
clus                  0   1
  PIK3C2B MUTATED     0  15
  PIK3C2B WILD-TYPE   6 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2B MUTATED      0   15
  PIK3C2B WILD-TYPE    6  334
                        clus
vv                       PIK3C2B MUTATED PIK3C2B WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              15               334
[1] 2 2
[1] FALSE

Clustering(317) Variable = FTSJ1 MUTATION ANALYSIS
D317V1, survival
                 sevent
clus2               0   1
  FTSJ1 MUTATED     5   2
  FTSJ1 WILD-TYPE 310 139
  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
              7             449 
  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
              2             139 
$`FTSJ1 MUTATED`
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-8094 TCGA-78-7156 TCGA-86-A4JF TCGA-91-6829 
        9.21        48.62         0.13        32.09        17.62        41.36 
TCGA-97-7937 
        5.95 

$`FTSJ1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        23.05         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         5.06        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79        25.48         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
           0.13            0.00 
  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
          48.62          223.96 
  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
          17.62           18.08 
[1] "0.1 - 48.6 (17.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D317V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FTSJ1 MUTATED         0        1        2         1         1          0
  FTSJ1 WILD-TYPE       4      122      131        45        66         70
                 vv
clus              STAGE IIIB STAGE IV
  FTSJ1 MUTATED            0        2
  FTSJ1 WILD-TYPE         11       23
D317V3, multiclass
            clus
vv           FTSJ1 MUTATED FTSJ1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               2             131
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FTSJ1 MUTATED     1   4   1   1
  FTSJ1 WILD-TYPE 154 257  42  17
D317V4, multiclass
    clus
vv   FTSJ1 MUTATED FTSJ1 WILD-TYPE
  T1             1             154
  T2             4             257
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  FTSJ1 MUTATED     5   2     0
  FTSJ1 WILD-TYPE 302  87    72
D317V5, multiclass
       clus
vv      FTSJ1 MUTATED FTSJ1 WILD-TYPE
  N0                5             302
  N1                2              87
  N2+N3             0              72
[1] 3 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
  FTSJ1 MUTATED     2   2
  FTSJ1 WILD-TYPE 325  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FTSJ1 MUTATED      2    2
  FTSJ1 WILD-TYPE  325   21
   clus
vv  FTSJ1 MUTATED FTSJ1 WILD-TYPE
  0             2             325
  1             2              21
[1] 2 2
[1] FALSE
D317V7, binary
                 cls
clus                0   1
  FTSJ1 MUTATED     1   6
  FTSJ1 WILD-TYPE 258 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FTSJ1 MUTATED      1    6
  FTSJ1 WILD-TYPE  258  215
        clus
vv       FTSJ1 MUTATED FTSJ1 WILD-TYPE
  FEMALE             1             258
  MALE               6             215
[1] 2 2
[1] FALSE
D317V8, continuous
[1] "Remove cluster labels:" "FTSJ1 MUTATED"         
clus
  FTSJ1 MUTATED FTSJ1 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-55-7283 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"FTSJ1 WILD-TYPE" "FTSJ1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FTSJ1 MUTATED                            1                                 1
  FTSJ1 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FTSJ1 MUTATED                                                    2
  FTSJ1 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FTSJ1 MUTATED                                            0
  FTSJ1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FTSJ1 MUTATED                                               1
  FTSJ1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FTSJ1 MUTATED                                1
  FTSJ1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FTSJ1 MUTATED                                    1
  FTSJ1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FTSJ1 MUTATED                              0                             0
  FTSJ1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FTSJ1 MUTATED                                               0
  FTSJ1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FTSJ1 MUTATED                              0
  FTSJ1 WILD-TYPE                            9
D317V9, multiclass
                                                    clus
vv                                                   FTSJ1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FTSJ1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V10, binary
                 cls
clus                0   1
  FTSJ1 MUTATED     0   7
  FTSJ1 WILD-TYPE  20 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FTSJ1 MUTATED      0    7
  FTSJ1 WILD-TYPE   20  453
     clus
vv    FTSJ1 MUTATED FTSJ1 WILD-TYPE
  NO              0              20
  YES             7             453
[1] 2 2
[1] FALSE
D317V11, continuous
D317V12, continuous
                 vv
clus               R0  R1  R2  RX
  FTSJ1 MUTATED     4   0   0   1
  FTSJ1 WILD-TYPE 306  11   4  24
D317V13, multiclass
    clus
vv   FTSJ1 MUTATED FTSJ1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FTSJ1 MUTATED                                  0     1
  FTSJ1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FTSJ1 MUTATED                           0     6
  FTSJ1 WILD-TYPE                        29   371
D317V14, multiclass
                                  clus
vv                                 FTSJ1 MUTATED FTSJ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V15, binary
                 cls
clus                0   1
  FTSJ1 MUTATED     1   5
  FTSJ1 WILD-TYPE   5 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FTSJ1 MUTATED      1    5
  FTSJ1 WILD-TYPE    5  344
                        clus
vv                       FTSJ1 MUTATED FTSJ1 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(318) Variable = IFNA6 MUTATION ANALYSIS
D318V1, survival
                 sevent
clus2               0   1
  IFNA6 MUTATED     6   0
  IFNA6 WILD-TYPE 309 141
  IFNA6 MUTATED IFNA6 WILD-TYPE 
              6             450 
  IFNA6 MUTATED IFNA6 WILD-TYPE 
              0             141 
$`IFNA6 MUTATED`
TCGA-44-6776 TCGA-44-7672 TCGA-50-5049 TCGA-55-6969 TCGA-55-8301 TCGA-86-8073 
       63.72        23.64        70.55        40.73         1.45        24.33 

$`IFNA6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
        9.93        27.78        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        29.00        17.59        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        22.16        15.42         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  IFNA6 MUTATED IFNA6 WILD-TYPE 
           1.45            0.00 
  IFNA6 MUTATED IFNA6 WILD-TYPE 
          70.55          223.96 
  IFNA6 MUTATED IFNA6 WILD-TYPE 
         32.530          17.835 
[1] "1.4 - 70.5 (32.5)"  "0.0 - 224.0 (17.8)"
[1] "hr="     "9300000"
D318V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IFNA6 MUTATED         0        3        3         0         0          0
  IFNA6 WILD-TYPE       4      120      130        46        67         70
                 vv
clus              STAGE IIIB STAGE IV
  IFNA6 MUTATED            0        0
  IFNA6 WILD-TYPE         11       25
D318V3, multiclass
            clus
vv           IFNA6 MUTATED IFNA6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFNA6 MUTATED     2   4   0   0
  IFNA6 WILD-TYPE 153 257  43  18
D318V4, multiclass
    clus
vv   IFNA6 MUTATED IFNA6 WILD-TYPE
  T1             2             153
  T2             4             257
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  IFNA6 MUTATED     6   0     0
  IFNA6 WILD-TYPE 301  89    72
D318V5, multiclass
       clus
vv      IFNA6 MUTATED IFNA6 WILD-TYPE
  N0                6             301
  N1                0              89
  N2+N3             0              72
[1] 3 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
  IFNA6 MUTATED     4   0
  IFNA6 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA6 MUTATED      4    0
  IFNA6 WILD-TYPE  323   23
   clus
vv  IFNA6 MUTATED IFNA6 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D318V7, binary
                 cls
clus                0   1
  IFNA6 MUTATED     2   4
  IFNA6 WILD-TYPE 257 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA6 MUTATED      2    4
  IFNA6 WILD-TYPE  257  217
        clus
vv       IFNA6 MUTATED IFNA6 WILD-TYPE
  FEMALE             2             257
  MALE               4             217
[1] 2 2
[1] FALSE
D318V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  IFNA6 MUTATED                            0                                 0
  IFNA6 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IFNA6 MUTATED                                                    5
  IFNA6 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IFNA6 MUTATED                                            0
  IFNA6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IFNA6 MUTATED                                               1
  IFNA6 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  IFNA6 MUTATED                                0
  IFNA6 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  IFNA6 MUTATED                                    0
  IFNA6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  IFNA6 MUTATED                              0                             0
  IFNA6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IFNA6 MUTATED                                               0
  IFNA6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  IFNA6 MUTATED                              0
  IFNA6 WILD-TYPE                            9
D318V9, multiclass
                                                    clus
vv                                                   IFNA6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   IFNA6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V10, binary
                 cls
clus                0   1
  IFNA6 MUTATED     1   5
  IFNA6 WILD-TYPE  19 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA6 MUTATED      1    5
  IFNA6 WILD-TYPE   19  455
     clus
vv    IFNA6 MUTATED IFNA6 WILD-TYPE
  NO              1              19
  YES             5             455
[1] 2 2
[1] FALSE
D318V11, continuous
D318V12, continuous
                 vv
clus               R0  R1  R2  RX
  IFNA6 MUTATED     2   0   0   0
  IFNA6 WILD-TYPE 308  11   4  25
D318V13, multiclass
[1] "Remove cluster labels:" "IFNA6 MUTATED"         
clus
  IFNA6 MUTATED IFNA6 WILD-TYPE 
              2             348 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4395 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-4396      TCGA-05-4397      TCGA-05-4398      TCGA-05-4402 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-4403      TCGA-05-4405      TCGA-05-4410      TCGA-05-4415 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-4417      TCGA-05-4418      TCGA-05-4420      TCGA-05-4422 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-4424      TCGA-05-4425      TCGA-05-4426      TCGA-05-4427 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-4430      TCGA-05-4432      TCGA-05-4433      TCGA-05-4434 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-5420      TCGA-05-5423      TCGA-05-5425      TCGA-05-5428 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-05-5429      TCGA-05-5715      TCGA-35-4122      TCGA-35-4123 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-4627 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-38-4628      TCGA-38-4629      TCGA-38-4630      TCGA-38-4631 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-38-4632      TCGA-38-6178      TCGA-38-7271      TCGA-38-A44F 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2661      TCGA-44-2665      TCGA-44-3396 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-3919      TCGA-44-4112 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6148      TCGA-44-6775      TCGA-44-A479 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47G      TCGA-44-A4SU 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4488      TCGA-49-4494 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-49-4501      TCGA-49-4505      TCGA-49-4506      TCGA-49-4507 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-49-4510      TCGA-49-4512      TCGA-49-4514      TCGA-49-6742 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-49-6744      TCGA-49-6761      TCGA-49-6767      TCGA-50-5051 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-50-5055      TCGA-50-5066      TCGA-50-5931      TCGA-50-5942 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-50-5944      TCGA-50-6593      TCGA-50-6597      TCGA-50-6673 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-50-8460      TCGA-53-7624      TCGA-53-7626      TCGA-53-A4EZ 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-5899      TCGA-55-6642      TCGA-55-6970 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-6971      TCGA-55-6972      TCGA-55-6980      TCGA-55-6981 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-6983      TCGA-55-6985      TCGA-55-7281      TCGA-55-7284 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7727      TCGA-55-7728 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-7815      TCGA-55-7903      TCGA-55-7907      TCGA-55-7910 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-7911      TCGA-55-7914      TCGA-55-7994      TCGA-55-7995 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8085      TCGA-55-8087      TCGA-55-8089      TCGA-55-8090 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8091      TCGA-55-8092      TCGA-55-8094      TCGA-55-8097 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8203      TCGA-55-8204      TCGA-55-8205      TCGA-55-8206 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8207      TCGA-55-8208      TCGA-55-8299      TCGA-55-8302 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8505      TCGA-55-8506      TCGA-55-8507      TCGA-55-8508 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8510      TCGA-55-8511      TCGA-55-8512      TCGA-55-8513 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8614      TCGA-55-8615      TCGA-55-8616 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-55-A4DG      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1676      TCGA-64-1677      TCGA-64-1679 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5774      TCGA-64-5775      TCGA-64-5778 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-64-5779      TCGA-64-5781      TCGA-64-5815      TCGA-67-3771 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-67-3773      TCGA-67-4679      TCGA-67-6215      TCGA-67-6216 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-67-6217      TCGA-71-6725      TCGA-71-8520      TCGA-73-4658 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-73-4670      TCGA-73-4675      TCGA-73-4676      TCGA-73-4677 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-75-5125 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-75-5126      TCGA-75-5146      TCGA-75-5147      TCGA-75-6203 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-75-6205      TCGA-75-6206      TCGA-75-6207      TCGA-75-6211 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-75-6212      TCGA-75-6214      TCGA-75-7025      TCGA-75-7027 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-75-7030      TCGA-75-7031      TCGA-78-7143      TCGA-78-7145 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-7146      TCGA-78-7147      TCGA-78-7148      TCGA-78-7149 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-7150      TCGA-78-7152      TCGA-78-7153      TCGA-78-7154 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-7155      TCGA-78-7156      TCGA-78-7158      TCGA-78-7159 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-7160      TCGA-78-7161      TCGA-78-7162      TCGA-78-7163 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-7166      TCGA-78-7167      TCGA-78-7220      TCGA-78-7535 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-7536      TCGA-78-7537      TCGA-78-7539      TCGA-78-7540 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-80-5608      TCGA-80-5611      TCGA-83-5908      TCGA-86-6562 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-86-7953      TCGA-86-7954      TCGA-86-7955      TCGA-86-8054 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8585      TCGA-86-8668 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8671      TCGA-86-8672      TCGA-86-8673 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-91-6828      TCGA-91-6829      TCGA-91-6835      TCGA-91-6840 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-91-A4BD      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JP      TCGA-93-A4JQ 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-95-8039      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-97-7546 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-97-7554      TCGA-97-7938      TCGA-97-7941      TCGA-97-8176 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-99-8028      TCGA-99-8032      TCGA-99-8033      TCGA-J2-A4AD 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-J2-A4AE      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-MP-A4T8      TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
     TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YQ 
"IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" "IFNA6 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFNA6 MUTATED                                  0     0
  IFNA6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFNA6 MUTATED                           0     6
  IFNA6 WILD-TYPE                        29   371
D318V14, multiclass
                                  clus
vv                                 IFNA6 MUTATED IFNA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V15, binary
                 cls
clus                0   1
  IFNA6 MUTATED     0   4
  IFNA6 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA6 MUTATED      0    4
  IFNA6 WILD-TYPE    6  345
                        clus
vv                       IFNA6 MUTATED IFNA6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(319) Variable = MME MUTATION ANALYSIS
D319V1, survival
               sevent
clus2             0   1
  MME MUTATED    11   2
  MME WILD-TYPE 304 139
  MME MUTATED MME WILD-TYPE 
           13           443 
  MME MUTATED MME WILD-TYPE 
            2           139 
$`MME MUTATED`
TCGA-38-4631 TCGA-44-7670 TCGA-55-1595 TCGA-55-7994 TCGA-55-7995 TCGA-55-8299 
       11.64        29.00        48.62        19.82         0.16        15.42 
TCGA-55-8301 TCGA-73-4666 TCGA-73-4670 TCGA-86-8358 TCGA-91-6830 TCGA-95-7567 
        1.45        26.30         4.31        21.47         1.97        18.67 
TCGA-NJ-A4YP 
        1.64 

$`MME WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
        2.17        22.16         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       29.98        15.35         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  MME MUTATED MME WILD-TYPE 
         0.16          0.00 
  MME MUTATED MME WILD-TYPE 
        48.62        223.96 
  MME MUTATED MME WILD-TYPE 
        15.42         18.08 
[1] "0.2 - 48.6 (15.4)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D319V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MME MUTATED         0        3        5         2         2          0
  MME WILD-TYPE       4      120      128        44        65         70
               vv
clus            STAGE IIIB STAGE IV
  MME MUTATED            0        2
  MME WILD-TYPE         11       23
D319V3, multiclass
            clus
vv           MME MUTATED MME WILD-TYPE
  STAGE I              0             4
  STAGE IA             3           120
  STAGE IB             5           128
  STAGE IIA            2            44
  STAGE IIB            2            65
  STAGE IIIA           0            70
  STAGE IIIB           0            11
  STAGE IV             2            23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MME MUTATED     6   7   1   0
  MME WILD-TYPE 149 254  42  18
D319V4, multiclass
    clus
vv   MME MUTATED MME WILD-TYPE
  T1           6           149
  T2           7           254
  T3           1            42
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  MME MUTATED    11   3     0
  MME WILD-TYPE 296  86    72
D319V5, multiclass
       clus
vv      MME MUTATED MME WILD-TYPE
  N0             11           296
  N1              3            86
  N2+N3           0            72
[1] 3 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
  MME MUTATED     8   2
  MME WILD-TYPE 319  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  MME MUTATED      8    2
  MME WILD-TYPE  319   21
   clus
vv  MME MUTATED MME WILD-TYPE
  0           8           319
  1           2            21
[1] 2 2
[1] FALSE
D319V7, binary
               cls
clus              0   1
  MME MUTATED     9   5
  MME WILD-TYPE 250 216
[1] "tbl2"
               cls
clus            [,1] [,2]
  MME MUTATED      9    5
  MME WILD-TYPE  250  216
        clus
vv       MME MUTATED MME WILD-TYPE
  FEMALE           9           250
  MALE             5           216
[1] 2 2
[1] FALSE
D319V8, continuous
[1] "Remove cluster labels:" "MME MUTATED"           
clus
  MME MUTATED MME WILD-TYPE 
            2            82 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-62-A470    TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-64-5778    TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-73-4659    TCGA-73-4662    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-86-8279    TCGA-86-8281    TCGA-86-8359    TCGA-86-8668    TCGA-86-8669 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849    TCGA-93-7348 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458    TCGA-MN-A4N1 
"MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" "MME WILD-TYPE" 
   TCGA-MN-A4N4    TCGA-MN-A4N5 
"MME WILD-TYPE" "MME WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MME MUTATED                            0                                 1
  MME WILD-TYPE                         18                               101
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MME MUTATED                                                   11
  MME WILD-TYPE                                                283
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MME MUTATED                                            0
  MME WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MME MUTATED                                               0
  MME WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MME MUTATED                                1
  MME WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MME MUTATED                                    0                            0
  MME WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MME MUTATED                               1
  MME WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MME MUTATED                                               0
  MME WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MME MUTATED                              0
  MME WILD-TYPE                            9
D319V9, multiclass
                                                    clus
vv                                                   MME MUTATED MME WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            1           101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          11           283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V10, binary
               cls
clus              0   1
  MME MUTATED     1  13
  MME WILD-TYPE  19 447
[1] "tbl2"
               cls
clus            [,1] [,2]
  MME MUTATED      1   13
  MME WILD-TYPE   19  447
     clus
vv    MME MUTATED MME WILD-TYPE
  NO            1            19
  YES          13           447
[1] 2 2
[1] FALSE
D319V11, continuous
D319V12, continuous
               vv
clus             R0  R1  R2  RX
  MME MUTATED     9   0   0   0
  MME WILD-TYPE 301  11   4  25
D319V13, multiclass
    clus
vv   MME MUTATED MME WILD-TYPE
  R0           9           301
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MME MUTATED                                  0     1
  MME WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MME MUTATED                           0    12
  MME WILD-TYPE                        29   365
D319V14, multiclass
                                  clus
vv                                 MME MUTATED MME WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                     12           365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V15, binary
               cls
clus              0   1
  MME MUTATED     1  12
  MME WILD-TYPE   5 337
[1] "tbl2"
               cls
clus            [,1] [,2]
  MME MUTATED      1   12
  MME WILD-TYPE    5  337
                        clus
vv                       MME MUTATED MME WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          12           337
[1] 2 2
[1] FALSE

Clustering(320) Variable = HYDIN MUTATION ANALYSIS
D320V1, survival
                 sevent
clus2               0   1
  HYDIN MUTATED    36  12
  HYDIN WILD-TYPE 279 129
  HYDIN MUTATED HYDIN WILD-TYPE 
             48             408 
  HYDIN MUTATED HYDIN WILD-TYPE 
             12             129 
$`HYDIN MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4422 TCGA-05-4430 
       19.96         9.96        47.05        20.05        12.00        25.02 
TCGA-38-4632 TCGA-44-2656 TCGA-44-3918 TCGA-44-7670 TCGA-44-8119 TCGA-44-8120 
       44.61        46.98        34.06        29.00         3.25         8.55 
TCGA-44-A479 TCGA-44-A47F TCGA-49-6743 TCGA-50-6594 TCGA-50-7109 TCGA-55-1595 
       15.98        11.08        12.13        12.16        10.13        48.62 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7907 TCGA-55-8089 TCGA-55-8302 TCGA-55-8510 
        0.59         0.20         0.53         3.29         0.76        17.72 
TCGA-55-8511 TCGA-62-8399 TCGA-62-A46R TCGA-64-5781 TCGA-69-7974 TCGA-69-7978 
        0.30        88.64        56.71        51.25         6.05         2.30 
TCGA-73-4662 TCGA-73-4670 TCGA-78-7220 TCGA-78-7536 TCGA-86-7713 TCGA-86-8278 
       29.98         4.31        26.53         8.02        13.87        15.65 
TCGA-93-7347 TCGA-95-7039 TCGA-95-A4VP TCGA-97-7938 TCGA-97-8547 TCGA-L9-A443 
        9.76         1.12        19.89         0.59        21.60         3.81 
TCGA-MN-A4N4 TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4TA TCGA-MP-A4TK TCGA-NJ-A4YQ 
       38.63        49.35        86.04        31.23        19.13        29.13 

$`HYDIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
       24.03         8.02        19.00         2.99        14.96         9.01 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 
       29.98        30.02        21.99        26.01        26.01        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       17.59        23.64        12.66        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        14.63        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 
       34.29        30.54        13.94         9.21        23.05         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
       70.26         1.74         1.15         7.99         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78         1.45        18.64         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.51         2.17        22.16        15.42         1.45         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.36         0.26         0.49         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S 
       42.38        14.60        49.25        47.80        19.53        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       13.61         5.42         7.56         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       23.38        26.30        15.35         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 
      104.19       223.96         8.48        88.14        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       16.08        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
       18.08        35.47        16.44        19.00        14.30         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 
       27.19         2.76        86.14        58.45        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        14.10        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  HYDIN MUTATED HYDIN WILD-TYPE 
            0.2             0.0 
  HYDIN MUTATED HYDIN WILD-TYPE 
          88.64          223.96 
  HYDIN MUTATED HYDIN WILD-TYPE 
         15.815          18.150 
[1] "0.2 - 88.6 (15.8)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D320V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HYDIN MUTATED         0       13       12         3         8          9
  HYDIN WILD-TYPE       4      110      121        43        59         61
                 vv
clus              STAGE IIIB STAGE IV
  HYDIN MUTATED            2        2
  HYDIN WILD-TYPE          9       23
D320V3, multiclass
            clus
vv           HYDIN MUTATED HYDIN WILD-TYPE
  STAGE I                0               4
  STAGE IA              13             110
  STAGE IB              12             121
  STAGE IIA              3              43
  STAGE IIB              8              59
  STAGE IIIA             9              61
  STAGE IIIB             2               9
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HYDIN MUTATED    15  29   3   2
  HYDIN WILD-TYPE 140 232  40  16
D320V4, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  T1            15             140
  T2            29             232
  T3             3              40
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  HYDIN MUTATED    29  10    10
  HYDIN WILD-TYPE 278  79    62
D320V5, multiclass
       clus
vv      HYDIN MUTATED HYDIN WILD-TYPE
  N0               29             278
  N1               10              79
  N2+N3            10              62
[1] 3 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
  HYDIN MUTATED    32   2
  HYDIN WILD-TYPE 295  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     32    2
  HYDIN WILD-TYPE  295   21
   clus
vv  HYDIN MUTATED HYDIN WILD-TYPE
  0            32             295
  1             2              21
[1] 2 2
[1] FALSE
D320V7, binary
                 cls
clus                0   1
  HYDIN MUTATED    30  19
  HYDIN WILD-TYPE 229 202
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     30   19
  HYDIN WILD-TYPE  229  202
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  FEMALE            30             229
  MALE              19             202
[1] 2 2
[1] FALSE
D320V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HYDIN MUTATED                            1                                14
  HYDIN WILD-TYPE                         17                                88
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HYDIN MUTATED                                                   30
  HYDIN WILD-TYPE                                                264
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HYDIN MUTATED                                            0
  HYDIN WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HYDIN MUTATED                                               1
  HYDIN WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HYDIN MUTATED                                2
  HYDIN WILD-TYPE                              0
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HYDIN MUTATED                                    0
  HYDIN WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HYDIN MUTATED                              0                             1
  HYDIN WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HYDIN MUTATED                                               0
  HYDIN WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HYDIN MUTATED                              0
  HYDIN WILD-TYPE                            9
D320V9, multiclass
                                                    clus
vv                                                   HYDIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HYDIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             264
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V10, binary
                 cls
clus                0   1
  HYDIN MUTATED     3  46
  HYDIN WILD-TYPE  17 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED      3   46
  HYDIN WILD-TYPE   17  414
     clus
vv    HYDIN MUTATED HYDIN WILD-TYPE
  NO              3              17
  YES            46             414
[1] 2 2
[1] FALSE
D320V11, continuous
D320V12, continuous
                 vv
clus               R0  R1  R2  RX
  HYDIN MUTATED    34   0   0   1
  HYDIN WILD-TYPE 276  11   4  24
D320V13, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  R0            34             276
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HYDIN MUTATED                                  0     1
  HYDIN WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HYDIN MUTATED                           5    34
  HYDIN WILD-TYPE                        24   343
D320V14, multiclass
                                  clus
vv                                 HYDIN MUTATED HYDIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    5              24
  WHITE                                       34             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V15, binary
                 cls
clus                0   1
  HYDIN MUTATED     1  32
  HYDIN WILD-TYPE   5 317
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED      1   32
  HYDIN WILD-TYPE    5  317
                        clus
vv                       HYDIN MUTATED HYDIN WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            32             317
[1] 2 2
[1] FALSE

Clustering(321) Variable = ILF3 MUTATION ANALYSIS
D321V1, survival
                sevent
clus2              0   1
  ILF3 MUTATED     4   1
  ILF3 WILD-TYPE 311 140
  ILF3 MUTATED ILF3 WILD-TYPE 
             5            451 
  ILF3 MUTATED ILF3 WILD-TYPE 
             1            140 
$`ILF3 MUTATED`
TCGA-44-2656 TCGA-55-8514 TCGA-73-4668 TCGA-95-7043 TCGA-MP-A4SV 
       46.98         6.64        15.35         1.22        86.14 

$`ILF3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
        0.49        17.72         0.30         0.10         4.80        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
        3.81         0.20        27.19        38.63         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ILF3 MUTATED ILF3 WILD-TYPE 
          1.22           0.00 
  ILF3 MUTATED ILF3 WILD-TYPE 
         86.14         223.96 
  ILF3 MUTATED ILF3 WILD-TYPE 
         15.35          18.08 
[1] "1.2 - 86.1 (15.3)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.4"
D321V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ILF3 MUTATED         0        1        3         0         1          0
  ILF3 WILD-TYPE       4      122      130        46        66         70
                vv
clus             STAGE IIIB STAGE IV
  ILF3 MUTATED            0        0
  ILF3 WILD-TYPE         11       25
D321V3, multiclass
            clus
vv           ILF3 MUTATED ILF3 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              3            130
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ILF3 MUTATED     1   4   0   0
  ILF3 WILD-TYPE 154 257  43  18
D321V4, multiclass
    clus
vv   ILF3 MUTATED ILF3 WILD-TYPE
  T1            1            154
  T2            4            257
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  ILF3 MUTATED     4   1     0
  ILF3 WILD-TYPE 303  88    72
D321V5, multiclass
       clus
vv      ILF3 MUTATED ILF3 WILD-TYPE
  N0               4            303
  N1               1             88
  N2+N3            0             72
[1] 3 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
  ILF3 MUTATED     3   0
  ILF3 WILD-TYPE 324  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  ILF3 MUTATED      3    0
  ILF3 WILD-TYPE  324   23
   clus
vv  ILF3 MUTATED ILF3 WILD-TYPE
  0            3            324
  1            0             23
[1] 2 2
[1] FALSE
D321V7, binary
                cls
clus               0   1
  ILF3 MUTATED     3   2
  ILF3 WILD-TYPE 256 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  ILF3 MUTATED      3    2
  ILF3 WILD-TYPE  256  219
        clus
vv       ILF3 MUTATED ILF3 WILD-TYPE
  FEMALE            3            256
  MALE              2            219
[1] 2 2
[1] FALSE
D321V8, continuous
[1] "Remove cluster labels:" "ILF3 MUTATED"          
clus
  ILF3 MUTATED ILF3 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"ILF3 WILD-TYPE" "ILF3 WILD-TYPE" "ILF3 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ILF3 MUTATED                            0                                 1
  ILF3 WILD-TYPE                         18                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ILF3 MUTATED                                                    3
  ILF3 WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ILF3 MUTATED                                            0
  ILF3 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ILF3 MUTATED                                               0
  ILF3 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  ILF3 MUTATED                                0
  ILF3 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  ILF3 MUTATED                                    1
  ILF3 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ILF3 MUTATED                              0                             0
  ILF3 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ILF3 MUTATED                                               0
  ILF3 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  ILF3 MUTATED                              0
  ILF3 WILD-TYPE                            9
D321V9, multiclass
                                                    clus
vv                                                   ILF3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   ILF3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V10, binary
                cls
clus               0   1
  ILF3 MUTATED     0   5
  ILF3 WILD-TYPE  20 455
[1] "tbl2"
                cls
clus             [,1] [,2]
  ILF3 MUTATED      0    5
  ILF3 WILD-TYPE   20  455
     clus
vv    ILF3 MUTATED ILF3 WILD-TYPE
  NO             0             20
  YES            5            455
[1] 2 2
[1] FALSE
D321V11, continuous
D321V12, continuous
                vv
clus              R0  R1  R2  RX
  ILF3 MUTATED     3   0   0   0
  ILF3 WILD-TYPE 307  11   4  25
D321V13, multiclass
    clus
vv   ILF3 MUTATED ILF3 WILD-TYPE
  R0            3            307
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ILF3 MUTATED                                  1     0
  ILF3 WILD-TYPE                                0     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ILF3 MUTATED                           1     2
  ILF3 WILD-TYPE                        28   375
D321V14, multiclass
                                  clus
vv                                 ILF3 MUTATED ILF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       2            375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V15, binary
                cls
clus               0   1
  ILF3 MUTATED     0   4
  ILF3 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  ILF3 MUTATED      0    4
  ILF3 WILD-TYPE    6  345
                        clus
vv                       ILF3 MUTATED ILF3 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(322) Variable = METTL2B MUTATION ANALYSIS
D322V1, survival
                   sevent
clus2                 0   1
  METTL2B MUTATED     3   1
  METTL2B WILD-TYPE 312 140
  METTL2B MUTATED METTL2B WILD-TYPE 
                4               452 
  METTL2B MUTATED METTL2B WILD-TYPE 
                1               140 
$`METTL2B MUTATED`
TCGA-44-6778 TCGA-55-7994 TCGA-55-8299 TCGA-64-5781 
       61.28        19.82        15.42        51.25 

$`METTL2B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       32.45        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 
       17.98         1.08         1.51         2.17        22.16         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  METTL2B MUTATED METTL2B WILD-TYPE 
            15.42              0.00 
  METTL2B MUTATED METTL2B WILD-TYPE 
            61.28            223.96 
  METTL2B MUTATED METTL2B WILD-TYPE 
           35.535            17.950 
[1] "15.4 - 61.3 (35.5)" "0.0 - 224.0 (18.0)"
[1] "hr=" "2.3"
D322V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  METTL2B MUTATED         0        2        1         0         1          0
  METTL2B WILD-TYPE       4      121      132        46        66         70
                   vv
clus                STAGE IIIB STAGE IV
  METTL2B MUTATED            0        0
  METTL2B WILD-TYPE         11       25
D322V3, multiclass
            clus
vv           METTL2B MUTATED METTL2B WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 1               132
  STAGE IIA                0                46
  STAGE IIB                1                66
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  METTL2B MUTATED     2   1   1   0
  METTL2B WILD-TYPE 153 260  42  18
D322V4, multiclass
    clus
vv   METTL2B MUTATED METTL2B WILD-TYPE
  T1               2               153
  T2               1               260
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  METTL2B MUTATED     4   0     0
  METTL2B WILD-TYPE 303  89    72
D322V5, multiclass
       clus
vv      METTL2B MUTATED METTL2B WILD-TYPE
  N0                  4               303
  N1                  0                89
  N2+N3               0                72
[1] 3 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
  METTL2B MUTATED     1   0
  METTL2B WILD-TYPE 326  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METTL2B MUTATED      1    0
  METTL2B WILD-TYPE  326   23
   clus
vv  METTL2B MUTATED METTL2B WILD-TYPE
  0               1               326
  1               0                23
[1] 2 2
[1] FALSE
D322V7, binary
                   cls
clus                  0   1
  METTL2B MUTATED     2   2
  METTL2B WILD-TYPE 257 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METTL2B MUTATED      2    2
  METTL2B WILD-TYPE  257  219
        clus
vv       METTL2B MUTATED METTL2B WILD-TYPE
  FEMALE               2               257
  MALE                 2               219
[1] 2 2
[1] FALSE
D322V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  METTL2B MUTATED                            0
  METTL2B WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  METTL2B MUTATED                                   1
  METTL2B WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  METTL2B MUTATED                                                    3
  METTL2B WILD-TYPE                                                291
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  METTL2B MUTATED                                            0
  METTL2B WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  METTL2B MUTATED                                               0
  METTL2B WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  METTL2B MUTATED                                0
  METTL2B WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  METTL2B MUTATED                                    0
  METTL2B WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  METTL2B MUTATED                              0                             0
  METTL2B WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  METTL2B MUTATED                                               0
  METTL2B WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  METTL2B MUTATED                              0
  METTL2B WILD-TYPE                            9
D322V9, multiclass
                                                    clus
vv                                                   METTL2B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   METTL2B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V10, binary
                   cls
clus                  0   1
  METTL2B MUTATED     0   4
  METTL2B WILD-TYPE  20 456
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METTL2B MUTATED      0    4
  METTL2B WILD-TYPE   20  456
     clus
vv    METTL2B MUTATED METTL2B WILD-TYPE
  NO                0                20
  YES               4               456
[1] 2 2
[1] FALSE
D322V11, continuous
D322V12, continuous
                   vv
clus                 R0  R1  R2  RX
  METTL2B MUTATED     3   0   0   0
  METTL2B WILD-TYPE 307  11   4  25
D322V13, multiclass
    clus
vv   METTL2B MUTATED METTL2B WILD-TYPE
  R0               3               307
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METTL2B MUTATED                                  0     0
  METTL2B WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  METTL2B MUTATED                           1     3
  METTL2B WILD-TYPE                        28   374
D322V14, multiclass
                                  clus
vv                                 METTL2B MUTATED METTL2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          3               374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V15, binary
                   cls
clus                  0   1
  METTL2B MUTATED     0   3
  METTL2B WILD-TYPE   6 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METTL2B MUTATED      0    3
  METTL2B WILD-TYPE    6  346
                        clus
vv                       METTL2B MUTATED METTL2B WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               346
[1] 2 2
[1] FALSE

Clustering(323) Variable = ZNF511 MUTATION ANALYSIS
D323V1, survival
                  sevent
clus2                0   1
  ZNF511 MUTATED     5   3
  ZNF511 WILD-TYPE 310 138
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               8              448 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               3              138 
$`ZNF511 MUTATED`
TCGA-44-6777 TCGA-49-4507 TCGA-50-7109 TCGA-55-7281 TCGA-55-A491 TCGA-86-8054 
       32.45         8.81        10.13         0.59        20.58        24.49 
TCGA-86-8673 TCGA-93-7348 
       14.96         4.18 

$`ZNF511 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       12.66        35.54        46.72        14.07        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 
       11.05        12.16         6.21        41.69         0.72        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 
       24.99        40.54       107.21        70.26         1.74         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82         9.76         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ZNF511 MUTATED ZNF511 WILD-TYPE 
            0.59             0.00 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
           32.45           223.96 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
          12.545           18.100 
[1] "0.6 - 32.5 (12.5)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.3"
D323V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF511 MUTATED         0        4        3         0         1          1
  ZNF511 WILD-TYPE       4      119      130        46        66         69
                  vv
clus               STAGE IIIB STAGE IV
  ZNF511 MUTATED            0        0
  ZNF511 WILD-TYPE         11       25
D323V3, multiclass
            clus
vv           ZNF511 MUTATED ZNF511 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                3              130
  STAGE IIA               0               46
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF511 MUTATED     4   4   1   0
  ZNF511 WILD-TYPE 151 257  42  18
D323V4, multiclass
    clus
vv   ZNF511 MUTATED ZNF511 WILD-TYPE
  T1              4              151
  T2              4              257
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ZNF511 MUTATED     6   2     0
  ZNF511 WILD-TYPE 301  87    72
D323V5, multiclass
       clus
vv      ZNF511 MUTATED ZNF511 WILD-TYPE
  N0                 6              301
  N1                 2               87
  N2+N3              0               72
[1] 3 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
  ZNF511 MUTATED     6   0
  ZNF511 WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF511 MUTATED      6    0
  ZNF511 WILD-TYPE  321   23
   clus
vv  ZNF511 MUTATED ZNF511 WILD-TYPE
  0              6              321
  1              0               23
[1] 2 2
[1] FALSE
D323V7, binary
                  cls
clus                 0   1
  ZNF511 MUTATED     5   4
  ZNF511 WILD-TYPE 254 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF511 MUTATED      5    4
  ZNF511 WILD-TYPE  254  217
        clus
vv       ZNF511 MUTATED ZNF511 WILD-TYPE
  FEMALE              5              254
  MALE                4              217
[1] 2 2
[1] FALSE
D323V8, continuous
[1] "Remove cluster labels:" "ZNF511 MUTATED"        
clus
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8279       TCGA-86-8281 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8669 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-86-8671       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF511 MUTATED                            1                                 1
  ZNF511 WILD-TYPE                         17                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF511 MUTATED                                                    6
  ZNF511 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF511 MUTATED                                            0
  ZNF511 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF511 MUTATED                                               1
  ZNF511 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF511 MUTATED                                0
  ZNF511 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF511 MUTATED                                    0
  ZNF511 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF511 MUTATED                              0                             0
  ZNF511 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF511 MUTATED                                               0
  ZNF511 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF511 MUTATED                              0
  ZNF511 WILD-TYPE                            9
D323V9, multiclass
                                                    clus
vv                                                   ZNF511 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF511 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V10, binary
                  cls
clus                 0   1
  ZNF511 MUTATED     2   7
  ZNF511 WILD-TYPE  18 453
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF511 MUTATED      2    7
  ZNF511 WILD-TYPE   18  453
     clus
vv    ZNF511 MUTATED ZNF511 WILD-TYPE
  NO               2               18
  YES              7              453
[1] 2 2
[1] FALSE
D323V11, continuous
D323V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF511 MUTATED     6   0   0   1
  ZNF511 WILD-TYPE 304  11   4  24
D323V13, multiclass
    clus
vv   ZNF511 MUTATED ZNF511 WILD-TYPE
  R0              6              304
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF511 MUTATED                                  0     0
  ZNF511 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF511 MUTATED                           0     8
  ZNF511 WILD-TYPE                        29   369
D323V14, multiclass
                                  clus
vv                                 ZNF511 MUTATED ZNF511 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         8              369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V15, binary
                  cls
clus                 0   1
  ZNF511 MUTATED     0   6
  ZNF511 WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF511 MUTATED      0    6
  ZNF511 WILD-TYPE    6  343
                        clus
vv                       ZNF511 MUTATED ZNF511 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              343
[1] 2 2
[1] FALSE

Clustering(324) Variable = U2AF1L4 MUTATION ANALYSIS
D324V1, survival
                   sevent
clus2                 0   1
  U2AF1L4 MUTATED     5   0
  U2AF1L4 WILD-TYPE 310 141
  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
                5               451 
  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
                0               141 
$`U2AF1L4 MUTATED`
TCGA-86-8073 TCGA-86-8358 TCGA-95-7567 TCGA-95-7944 TCGA-NJ-A4YQ 
       24.33        21.47        18.67        12.39        29.13 

$`U2AF1L4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
       17.29         1.12         1.22         2.86        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
            12.39              0.00 
  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
            29.13            223.96 
  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
            21.47             17.92 
[1] "12.4 - 29.1 (21.5)" "0.0 - 224.0 (17.9)"
[1] "hr="     "3300000"
D324V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  U2AF1L4 MUTATED         0        2        2         0         1          0
  U2AF1L4 WILD-TYPE       4      121      131        46        66         70
                   vv
clus                STAGE IIIB STAGE IV
  U2AF1L4 MUTATED            0        0
  U2AF1L4 WILD-TYPE         11       25
D324V3, multiclass
            clus
vv           U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 2               131
  STAGE IIA                0                46
  STAGE IIB                1                66
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  U2AF1L4 MUTATED     2   3   0   0
  U2AF1L4 WILD-TYPE 153 258  43  18
D324V4, multiclass
    clus
vv   U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  T1               2               153
  T2               3               258
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  U2AF1L4 MUTATED     4   1     0
  U2AF1L4 WILD-TYPE 303  88    72
D324V5, multiclass
       clus
vv      U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  N0                  4               303
  N1                  1                88
  N2+N3               0                72
[1] 3 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
  U2AF1L4 MUTATED     5   0
  U2AF1L4 WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  U2AF1L4 MUTATED      5    0
  U2AF1L4 WILD-TYPE  322   23
   clus
vv  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  0               5               322
  1               0                23
[1] 2 2
[1] FALSE
D324V7, binary
                   cls
clus                  0   1
  U2AF1L4 MUTATED     1   4
  U2AF1L4 WILD-TYPE 258 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  U2AF1L4 MUTATED      1    4
  U2AF1L4 WILD-TYPE  258  217
        clus
vv       U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  FEMALE               1               258
  MALE                 4               217
[1] 2 2
[1] FALSE
D324V8, continuous
[1] "Remove cluster labels:" "U2AF1L4 MUTATED"       
clus
  U2AF1L4 MUTATED U2AF1L4 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" "U2AF1L4 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  U2AF1L4 MUTATED                            0
  U2AF1L4 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  U2AF1L4 MUTATED                                   1
  U2AF1L4 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  U2AF1L4 MUTATED                                                    3
  U2AF1L4 WILD-TYPE                                                291
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  U2AF1L4 MUTATED                                            0
  U2AF1L4 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  U2AF1L4 MUTATED                                               1
  U2AF1L4 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  U2AF1L4 MUTATED                                0
  U2AF1L4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  U2AF1L4 MUTATED                                    0
  U2AF1L4 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  U2AF1L4 MUTATED                              0                             0
  U2AF1L4 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  U2AF1L4 MUTATED                                               0
  U2AF1L4 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  U2AF1L4 MUTATED                              0
  U2AF1L4 WILD-TYPE                            9
D324V9, multiclass
                                                    clus
vv                                                   U2AF1L4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   U2AF1L4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V10, binary
                   cls
clus                  0   1
  U2AF1L4 MUTATED     0   5
  U2AF1L4 WILD-TYPE  20 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  U2AF1L4 MUTATED      0    5
  U2AF1L4 WILD-TYPE   20  455
     clus
vv    U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  NO                0                20
  YES               5               455
[1] 2 2
[1] FALSE
D324V11, continuous
D324V12, continuous
                   vv
clus                 R0  R1  R2  RX
  U2AF1L4 MUTATED     3   0   0   1
  U2AF1L4 WILD-TYPE 307  11   4  24
D324V13, multiclass
    clus
vv   U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  R0               3               307
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  U2AF1L4 MUTATED                                  0     0
  U2AF1L4 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  U2AF1L4 MUTATED                           0     5
  U2AF1L4 WILD-TYPE                        29   372
D324V14, multiclass
                                  clus
vv                                 U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          5               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V15, binary
                   cls
clus                  0   1
  U2AF1L4 MUTATED     0   5
  U2AF1L4 WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  U2AF1L4 MUTATED      0    5
  U2AF1L4 WILD-TYPE    6  344
                        clus
vv                       U2AF1L4 MUTATED U2AF1L4 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(325) Variable = HTR3D MUTATION ANALYSIS
D325V1, survival
                 sevent
clus2               0   1
  HTR3D MUTATED     3   1
  HTR3D WILD-TYPE 312 140
  HTR3D MUTATED HTR3D WILD-TYPE 
              4             452 
  HTR3D MUTATED HTR3D WILD-TYPE 
              1             140 
$`HTR3D MUTATED`
TCGA-53-A4EZ TCGA-55-8620 TCGA-91-6847 TCGA-97-8174 
        9.21         2.17        27.68         5.39 

$`HTR3D WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.58         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67        17.92        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  HTR3D MUTATED HTR3D WILD-TYPE 
           2.17            0.00 
  HTR3D MUTATED HTR3D WILD-TYPE 
          27.68          223.96 
  HTR3D MUTATED HTR3D WILD-TYPE 
            7.3            18.1 
[1] "2.2 - 27.7 (7.3)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "2.1"
D325V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HTR3D MUTATED         0        0        1         2         0          0
  HTR3D WILD-TYPE       4      123      132        44        67         70
                 vv
clus              STAGE IIIB STAGE IV
  HTR3D MUTATED            0        1
  HTR3D WILD-TYPE         11       24
D325V3, multiclass
            clus
vv           HTR3D MUTATED HTR3D WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               1             132
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HTR3D MUTATED     1   3   0   0
  HTR3D WILD-TYPE 154 258  43  18
D325V4, multiclass
    clus
vv   HTR3D MUTATED HTR3D WILD-TYPE
  T1             1             154
  T2             3             258
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  HTR3D MUTATED     2   2     0
  HTR3D WILD-TYPE 305  87    72
D325V5, multiclass
       clus
vv      HTR3D MUTATED HTR3D WILD-TYPE
  N0                2             305
  N1                2              87
  N2+N3             0              72
[1] 3 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
  HTR3D MUTATED     1   1
  HTR3D WILD-TYPE 326  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR3D MUTATED      1    1
  HTR3D WILD-TYPE  326   22
   clus
vv  HTR3D MUTATED HTR3D WILD-TYPE
  0             1             326
  1             1              22
[1] 2 2
[1] FALSE
D325V7, binary
                 cls
clus                0   1
  HTR3D MUTATED     1   3
  HTR3D WILD-TYPE 258 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR3D MUTATED      1    3
  HTR3D WILD-TYPE  258  218
        clus
vv       HTR3D MUTATED HTR3D WILD-TYPE
  FEMALE             1             258
  MALE               3             218
[1] 2 2
[1] FALSE
D325V8, continuous
[1] "Remove cluster labels:" "HTR3D MUTATED"         
clus
  HTR3D MUTATED HTR3D WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-55-7283 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8619      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HTR3D MUTATED                            1                                 0
  HTR3D WILD-TYPE                         17                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HTR3D MUTATED                                                    2
  HTR3D WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HTR3D MUTATED                                            0
  HTR3D WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HTR3D MUTATED                                               0
  HTR3D WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HTR3D MUTATED                                0
  HTR3D WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HTR3D MUTATED                                    0
  HTR3D WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HTR3D MUTATED                              0                             1
  HTR3D WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HTR3D MUTATED                                               0
  HTR3D WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HTR3D MUTATED                              0
  HTR3D WILD-TYPE                            9
D325V9, multiclass
                                                    clus
vv                                                   HTR3D MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HTR3D WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V10, binary
                 cls
clus                0   1
  HTR3D MUTATED     0   4
  HTR3D WILD-TYPE  20 456
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR3D MUTATED      0    4
  HTR3D WILD-TYPE   20  456
     clus
vv    HTR3D MUTATED HTR3D WILD-TYPE
  NO              0              20
  YES             4             456
[1] 2 2
[1] FALSE
D325V11, continuous
D325V12, continuous
                 vv
clus               R0  R1  R2  RX
  HTR3D MUTATED     1   0   0   1
  HTR3D WILD-TYPE 309  11   4  24
D325V13, multiclass
[1] "Remove cluster labels:" "HTR3D MUTATED"         
clus
  HTR3D MUTATED HTR3D WILD-TYPE 
              2             348 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4395 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-4396      TCGA-05-4397      TCGA-05-4398      TCGA-05-4402 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-4403      TCGA-05-4405      TCGA-05-4410      TCGA-05-4415 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-4417      TCGA-05-4418      TCGA-05-4420      TCGA-05-4422 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-4424      TCGA-05-4425      TCGA-05-4426      TCGA-05-4427 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-4430      TCGA-05-4432      TCGA-05-4433      TCGA-05-4434 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-5420      TCGA-05-5423      TCGA-05-5425      TCGA-05-5428 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-05-5429      TCGA-05-5715      TCGA-35-4122      TCGA-35-4123 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-4627 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-38-4628      TCGA-38-4629      TCGA-38-4630      TCGA-38-4631 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-38-4632      TCGA-38-6178      TCGA-38-7271      TCGA-38-A44F 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-44-2657      TCGA-44-2661      TCGA-44-2665      TCGA-44-3396 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-3919      TCGA-44-4112 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6148      TCGA-44-6775      TCGA-44-A479 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47G      TCGA-44-A4SU 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4488      TCGA-49-4494 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-49-4501      TCGA-49-4505      TCGA-49-4506      TCGA-49-4507 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-49-4510      TCGA-49-4512      TCGA-49-4514      TCGA-49-6742 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-49-6744      TCGA-49-6761      TCGA-49-6767      TCGA-50-5051 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-50-5055      TCGA-50-5066      TCGA-50-5931      TCGA-50-5942 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-50-5944      TCGA-50-6593      TCGA-50-6597      TCGA-50-6673 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-50-8460      TCGA-53-7624      TCGA-53-7626      TCGA-55-1592 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-5899      TCGA-55-6642      TCGA-55-6970      TCGA-55-6971 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-6972      TCGA-55-6980      TCGA-55-6981      TCGA-55-6983 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-6985      TCGA-55-7281      TCGA-55-7284      TCGA-55-7570 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7576      TCGA-55-7724      TCGA-55-7725 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-7726      TCGA-55-7727      TCGA-55-7728      TCGA-55-7815 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-7903      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-7914      TCGA-55-7994      TCGA-55-7995      TCGA-55-8085 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8087      TCGA-55-8089      TCGA-55-8090      TCGA-55-8091 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8097      TCGA-55-8203 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8204      TCGA-55-8205      TCGA-55-8206      TCGA-55-8207 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8505      TCGA-55-8506      TCGA-55-8507      TCGA-55-8508 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8510      TCGA-55-8511      TCGA-55-8512      TCGA-55-8513 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8614      TCGA-55-8615      TCGA-55-8616 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-64-1676      TCGA-64-1677      TCGA-64-1679      TCGA-64-1681 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-64-5774      TCGA-64-5775      TCGA-64-5778      TCGA-64-5779 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-64-5781      TCGA-64-5815      TCGA-67-3771      TCGA-67-3773 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-67-4679      TCGA-67-6215      TCGA-67-6216      TCGA-67-6217 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4658      TCGA-73-4659 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-4677      TCGA-73-7498 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-73-7499      TCGA-75-5122      TCGA-75-5125      TCGA-75-5126 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-75-5146      TCGA-75-5147      TCGA-75-6203      TCGA-75-6205 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-75-6206      TCGA-75-6207      TCGA-75-6211      TCGA-75-6212 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7030 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7143      TCGA-78-7145      TCGA-78-7146 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-7147      TCGA-78-7148      TCGA-78-7149      TCGA-78-7150 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-7152      TCGA-78-7153      TCGA-78-7154      TCGA-78-7155 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-7156      TCGA-78-7158      TCGA-78-7159      TCGA-78-7160 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-7161      TCGA-78-7162      TCGA-78-7163      TCGA-78-7166 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-7167      TCGA-78-7220      TCGA-78-7535      TCGA-78-7536 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-7537      TCGA-78-7539      TCGA-78-7540      TCGA-78-7542 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-7633      TCGA-78-8640      TCGA-78-8648      TCGA-78-8655 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-78-8660      TCGA-78-8662      TCGA-80-5607      TCGA-80-5608 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-80-5611      TCGA-83-5908      TCGA-86-6562      TCGA-86-7701 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7713      TCGA-86-7714      TCGA-86-7953 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8054      TCGA-86-8055 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8075 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8585      TCGA-86-8668 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8671      TCGA-86-8672      TCGA-86-8673 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-91-6828      TCGA-91-6829      TCGA-91-6835      TCGA-91-6840 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-91-A4BD      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JP      TCGA-93-A4JQ 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-95-8039      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-97-7546 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-97-7554      TCGA-97-7938      TCGA-97-7941      TCGA-97-8176 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-99-8028      TCGA-99-8032      TCGA-99-8033      TCGA-J2-A4AD 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-J2-A4AE      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-MP-A4T8      TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
     TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YQ 
"HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" "HTR3D WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HTR3D MUTATED                                  0     0
  HTR3D WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HTR3D MUTATED                           0     4
  HTR3D WILD-TYPE                        29   373
D325V14, multiclass
                                  clus
vv                                 HTR3D MUTATED HTR3D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V15, binary
                 cls
clus                0   1
  HTR3D MUTATED     1   3
  HTR3D WILD-TYPE   5 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR3D MUTATED      1    3
  HTR3D WILD-TYPE    5  346
                        clus
vv                       HTR3D MUTATED HTR3D WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             3             346
[1] 2 2
[1] FALSE

Clustering(326) Variable = EIF4E2 MUTATION ANALYSIS
D326V1, survival
                  sevent
clus2                0   1
  EIF4E2 MUTATED     3   1
  EIF4E2 WILD-TYPE 312 140
  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
               4              452 
  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
               1              140 
$`EIF4E2 MUTATED`
TCGA-44-8117 TCGA-50-6592 TCGA-95-7947 TCGA-L9-A444 
       12.66        25.55        15.68         0.20 

$`EIF4E2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
             0.2              0.0 
  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
           25.55           223.96 
  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
           14.17            18.10 
[1] "0.2 - 25.6 (14.2)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D326V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  EIF4E2 MUTATED         0        2        2         0         0          0
  EIF4E2 WILD-TYPE       4      121      131        46        67         70
                  vv
clus               STAGE IIIB STAGE IV
  EIF4E2 MUTATED            0        0
  EIF4E2 WILD-TYPE         11       25
D326V3, multiclass
            clus
vv           EIF4E2 MUTATED EIF4E2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                2              131
  STAGE IIA               0               46
  STAGE IIB               0               67
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF4E2 MUTATED     2   2   0   0
  EIF4E2 WILD-TYPE 153 259  43  18
D326V4, multiclass
    clus
vv   EIF4E2 MUTATED EIF4E2 WILD-TYPE
  T1              2              153
  T2              2              259
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  EIF4E2 MUTATED     4   0     0
  EIF4E2 WILD-TYPE 303  89    72
D326V5, multiclass
       clus
vv      EIF4E2 MUTATED EIF4E2 WILD-TYPE
  N0                 4              303
  N1                 0               89
  N2+N3              0               72
[1] 3 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
  EIF4E2 MUTATED     3   0
  EIF4E2 WILD-TYPE 324  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4E2 MUTATED      3    0
  EIF4E2 WILD-TYPE  324   23
   clus
vv  EIF4E2 MUTATED EIF4E2 WILD-TYPE
  0              3              324
  1              0               23
[1] 2 2
[1] FALSE
D326V7, binary
                  cls
clus                 0   1
  EIF4E2 MUTATED     3   1
  EIF4E2 WILD-TYPE 256 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4E2 MUTATED      3    1
  EIF4E2 WILD-TYPE  256  220
        clus
vv       EIF4E2 MUTATED EIF4E2 WILD-TYPE
  FEMALE              3              256
  MALE                1              220
[1] 2 2
[1] FALSE
D326V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EIF4E2 MUTATED                            0                                 1
  EIF4E2 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EIF4E2 MUTATED                                                    3
  EIF4E2 WILD-TYPE                                                291
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  EIF4E2 MUTATED                                            0
  EIF4E2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  EIF4E2 MUTATED                                               0
  EIF4E2 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  EIF4E2 MUTATED                                0
  EIF4E2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  EIF4E2 MUTATED                                    0
  EIF4E2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  EIF4E2 MUTATED                              0                             0
  EIF4E2 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  EIF4E2 MUTATED                                               0
  EIF4E2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  EIF4E2 MUTATED                              0
  EIF4E2 WILD-TYPE                            9
D326V9, multiclass
                                                    clus
vv                                                   EIF4E2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   EIF4E2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V10, binary
                  cls
clus                 0   1
  EIF4E2 MUTATED     0   4
  EIF4E2 WILD-TYPE  20 456
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4E2 MUTATED      0    4
  EIF4E2 WILD-TYPE   20  456
     clus
vv    EIF4E2 MUTATED EIF4E2 WILD-TYPE
  NO               0               20
  YES              4              456
[1] 2 2
[1] FALSE
D326V11, continuous
D326V12, continuous
                  vv
clus                R0  R1  R2  RX
  EIF4E2 MUTATED     2   0   0   0
  EIF4E2 WILD-TYPE 308  11   4  25
D326V13, multiclass
[1] "Remove cluster labels:" "EIF4E2 MUTATED"        
clus
  EIF4E2 MUTATED EIF4E2 WILD-TYPE 
               2              348 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-05-4382 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-4384       TCGA-05-4389       TCGA-05-4390       TCGA-05-4395 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-4396       TCGA-05-4397       TCGA-05-4398       TCGA-05-4402 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-4403       TCGA-05-4405       TCGA-05-4410       TCGA-05-4415 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-4417       TCGA-05-4418       TCGA-05-4420       TCGA-05-4422 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-4424       TCGA-05-4425       TCGA-05-4426       TCGA-05-4427 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-4430       TCGA-05-4432       TCGA-05-4433       TCGA-05-4434 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-5420       TCGA-05-5423       TCGA-05-5425       TCGA-05-5428 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-05-5429       TCGA-05-5715       TCGA-35-4122       TCGA-35-4123 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-35-5375       TCGA-38-4625       TCGA-38-4626       TCGA-38-4627 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-38-4628       TCGA-38-4629       TCGA-38-4630       TCGA-38-4631 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-6178       TCGA-38-7271       TCGA-38-A44F 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2661       TCGA-44-2665       TCGA-44-3396 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-44-3398       TCGA-44-3918       TCGA-44-3919       TCGA-44-4112 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6148       TCGA-44-6775       TCGA-44-A479 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SU 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4488       TCGA-49-4494 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-49-4501       TCGA-49-4505       TCGA-49-4506       TCGA-49-4507 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-49-4510       TCGA-49-4512       TCGA-49-4514       TCGA-49-6742 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-49-6744       TCGA-49-6761       TCGA-49-6767       TCGA-50-5051 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-50-5055       TCGA-50-5066       TCGA-50-5931       TCGA-50-5942 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-50-5944       TCGA-50-6593       TCGA-50-6597       TCGA-50-6673 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-50-8460       TCGA-53-7624       TCGA-53-7626       TCGA-53-A4EZ 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-1592       TCGA-55-5899       TCGA-55-6642       TCGA-55-6970 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-6971       TCGA-55-6972       TCGA-55-6980       TCGA-55-6981 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-6983       TCGA-55-6985       TCGA-55-7281       TCGA-55-7284 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-7570       TCGA-55-7574       TCGA-55-7576       TCGA-55-7724 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7727       TCGA-55-7728 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-7815       TCGA-55-7903       TCGA-55-7907       TCGA-55-7910 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-7911       TCGA-55-7914       TCGA-55-7994       TCGA-55-7995 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8085       TCGA-55-8087       TCGA-55-8089       TCGA-55-8090 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8091       TCGA-55-8092       TCGA-55-8094       TCGA-55-8097 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8206 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8207       TCGA-55-8208       TCGA-55-8299       TCGA-55-8301 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8302       TCGA-55-8505       TCGA-55-8506       TCGA-55-8507 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8510       TCGA-55-8511       TCGA-55-8512 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8513       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-8616       TCGA-55-8619       TCGA-55-8620       TCGA-55-8621 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A493       TCGA-55-A494 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-55-A4DF       TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1676       TCGA-64-1677 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-64-1679       TCGA-64-1681       TCGA-64-5774       TCGA-64-5775 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-64-5778       TCGA-64-5779       TCGA-64-5781       TCGA-64-5815 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-67-3771       TCGA-67-3773       TCGA-67-4679       TCGA-67-6215 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-67-6216       TCGA-67-6217       TCGA-71-6725       TCGA-71-8520 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-73-4658       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4670       TCGA-73-4675       TCGA-73-4676 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-73-4677       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-75-5125       TCGA-75-5126       TCGA-75-5146       TCGA-75-5147 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-75-6203       TCGA-75-6205       TCGA-75-6206       TCGA-75-6207 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-75-6211       TCGA-75-6212       TCGA-75-6214       TCGA-75-7025 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-75-7027       TCGA-75-7030       TCGA-75-7031       TCGA-78-7143 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-7145       TCGA-78-7146       TCGA-78-7147       TCGA-78-7148 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-7149       TCGA-78-7150       TCGA-78-7152       TCGA-78-7153 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-7154       TCGA-78-7155       TCGA-78-7156       TCGA-78-7158 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-7159       TCGA-78-7160       TCGA-78-7161       TCGA-78-7162 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-7163       TCGA-78-7166       TCGA-78-7167       TCGA-78-7220 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-7535       TCGA-78-7536       TCGA-78-7537       TCGA-78-7539 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-7540       TCGA-78-7542       TCGA-78-7633       TCGA-78-8640 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-78-8648       TCGA-78-8655       TCGA-78-8660       TCGA-78-8662 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-80-5607       TCGA-80-5608       TCGA-80-5611       TCGA-83-5908 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-6562       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7953       TCGA-86-7954       TCGA-86-7955 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-8054       TCGA-86-8055       TCGA-86-8056       TCGA-86-8073 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8280       TCGA-86-8358       TCGA-86-8359 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-8585       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-8672       TCGA-86-8673       TCGA-86-8674       TCGA-86-A456 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6828       TCGA-91-6829 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-91-6835       TCGA-91-6840       TCGA-91-A4BD       TCGA-93-7347 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-93-7348       TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-93-A4JP       TCGA-93-A4JQ       TCGA-95-7562       TCGA-95-7944 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-95-7948       TCGA-95-8039       TCGA-95-A4VK       TCGA-95-A4VN 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-97-7546       TCGA-97-7554       TCGA-97-7938       TCGA-97-7941 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-97-8176       TCGA-97-A4M2       TCGA-97-A4M7       TCGA-99-7458 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-99-8025       TCGA-99-8028       TCGA-99-8032       TCGA-99-8033 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-J2-A4AD       TCGA-J2-A4AE       TCGA-J2-A4AG       TCGA-L4-A4E5 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-L4-A4E6       TCGA-L9-A443       TCGA-MN-A4N1       TCGA-MN-A4N4 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T7 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-MP-A4T8       TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
      TCGA-MP-A4TI       TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YQ 
"EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" "EIF4E2 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF4E2 MUTATED                                  0     0
  EIF4E2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF4E2 MUTATED                           0     4
  EIF4E2 WILD-TYPE                        29   373
D326V14, multiclass
                                  clus
vv                                 EIF4E2 MUTATED EIF4E2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         4              373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V15, binary
                  cls
clus                 0   1
  EIF4E2 MUTATED     0   4
  EIF4E2 WILD-TYPE   6 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4E2 MUTATED      0    4
  EIF4E2 WILD-TYPE    6  345
                        clus
vv                       EIF4E2 MUTATED EIF4E2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(327) Variable = GAL3ST4 MUTATION ANALYSIS
D327V1, survival
                   sevent
clus2                 0   1
  GAL3ST4 MUTATED    10   1
  GAL3ST4 WILD-TYPE 305 140
  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
               11               445 
  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
                1               140 
$`GAL3ST4 MUTATED`
TCGA-05-4382 TCGA-44-3918 TCGA-44-8120 TCGA-55-6642 TCGA-55-6985 TCGA-55-8620 
       19.96        34.06         8.55        32.65        40.54         2.17 
TCGA-69-7973 TCGA-86-8073 TCGA-86-A4JF TCGA-91-6829 TCGA-95-A4VN 
        7.56        24.33        17.62        41.36        18.18 

$`GAL3ST4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
       27.58         0.62        14.96        13.32        13.32        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       27.29         2.76        21.40        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
             2.17              0.00 
  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
            41.36            223.96 
  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
            19.96             17.92 
[1] "2.2 - 41.4 (20.0)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "3.2"
D327V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GAL3ST4 MUTATED         0        1        7         1         1          0
  GAL3ST4 WILD-TYPE       4      122      126        45        66         70
                   vv
clus                STAGE IIIB STAGE IV
  GAL3ST4 MUTATED            0        1
  GAL3ST4 WILD-TYPE         11       24
D327V3, multiclass
            clus
vv           GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 7               126
  STAGE IIA                1                45
  STAGE IIB                1                66
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GAL3ST4 MUTATED     2   8   1   0
  GAL3ST4 WILD-TYPE 153 253  42  18
D327V4, multiclass
    clus
vv   GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  T1               2               153
  T2               8               253
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  GAL3ST4 MUTATED     9   2     0
  GAL3ST4 WILD-TYPE 298  87    72
D327V5, multiclass
       clus
vv      GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  N0                  9               298
  N1                  2                87
  N2+N3               0                72
[1] 3 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
  GAL3ST4 MUTATED     7   1
  GAL3ST4 WILD-TYPE 320  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GAL3ST4 MUTATED      7    1
  GAL3ST4 WILD-TYPE  320   22
   clus
vv  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  0               7               320
  1               1                22
[1] 2 2
[1] FALSE
D327V7, binary
                   cls
clus                  0   1
  GAL3ST4 MUTATED     4   7
  GAL3ST4 WILD-TYPE 255 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GAL3ST4 MUTATED      4    7
  GAL3ST4 WILD-TYPE  255  214
        clus
vv       GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  FEMALE               4               255
  MALE                 7               214
[1] 2 2
[1] FALSE
D327V8, continuous
[1] "Remove cluster labels:" "GAL3ST4 MUTATED"       
clus
  GAL3ST4 MUTATED GAL3ST4 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-A48Z        TCGA-55-A490 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"GAL3ST4 WILD-TYPE" "GAL3ST4 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  GAL3ST4 MUTATED                            0
  GAL3ST4 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  GAL3ST4 MUTATED                                   2
  GAL3ST4 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GAL3ST4 MUTATED                                                    6
  GAL3ST4 WILD-TYPE                                                288
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GAL3ST4 MUTATED                                            0
  GAL3ST4 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GAL3ST4 MUTATED                                               2
  GAL3ST4 WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  GAL3ST4 MUTATED                                0
  GAL3ST4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  GAL3ST4 MUTATED                                    0
  GAL3ST4 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GAL3ST4 MUTATED                              0                             0
  GAL3ST4 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GAL3ST4 MUTATED                                               1
  GAL3ST4 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  GAL3ST4 MUTATED                              0
  GAL3ST4 WILD-TYPE                            9
D327V9, multiclass
                                                    clus
vv                                                   GAL3ST4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   GAL3ST4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V10, binary
                   cls
clus                  0   1
  GAL3ST4 MUTATED     0  11
  GAL3ST4 WILD-TYPE  20 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GAL3ST4 MUTATED      0   11
  GAL3ST4 WILD-TYPE   20  449
     clus
vv    GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  NO                0                20
  YES              11               449
[1] 2 2
[1] FALSE
D327V11, continuous
D327V12, continuous
                   vv
clus                 R0  R1  R2  RX
  GAL3ST4 MUTATED     9   0   0   0
  GAL3ST4 WILD-TYPE 301  11   4  25
D327V13, multiclass
    clus
vv   GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  R0               9               301
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAL3ST4 MUTATED                                  0     0
  GAL3ST4 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GAL3ST4 MUTATED                           1     9
  GAL3ST4 WILD-TYPE                        28   368
D327V14, multiclass
                                  clus
vv                                 GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          9               368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V15, binary
                   cls
clus                  0   1
  GAL3ST4 MUTATED     0   8
  GAL3ST4 WILD-TYPE   6 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GAL3ST4 MUTATED      0    8
  GAL3ST4 WILD-TYPE    6  341
                        clus
vv                       GAL3ST4 MUTATED GAL3ST4 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               8               341
[1] 2 2
[1] FALSE

Clustering(328) Variable = MBD1 MUTATION ANALYSIS
D328V1, survival
                sevent
clus2              0   1
  MBD1 MUTATED     6   3
  MBD1 WILD-TYPE 309 138
  MBD1 MUTATED MBD1 WILD-TYPE 
             9            447 
  MBD1 MUTATED MBD1 WILD-TYPE 
             3            138 
$`MBD1 MUTATED`
TCGA-50-5941 TCGA-55-1592 TCGA-55-5899 TCGA-55-7910 TCGA-55-8208 TCGA-73-4662 
       18.64        23.05         2.86         6.48        22.16        29.98 
TCGA-78-7154 TCGA-78-7542 TCGA-86-8073 
       19.50        10.55        24.33 

$`MBD1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       15.12        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94         9.21        48.62         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         0.53        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
       31.20         8.02        53.33        10.75        39.35        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MBD1 MUTATED MBD1 WILD-TYPE 
          2.86           0.00 
  MBD1 MUTATED MBD1 WILD-TYPE 
         29.98         223.96 
  MBD1 MUTATED MBD1 WILD-TYPE 
         19.50          17.92 
[1] "2.9 - 30.0 (19.5)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.7"
D328V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MBD1 MUTATED         0        4        3         1         0          2
  MBD1 WILD-TYPE       4      119      130        45        67         68
                vv
clus             STAGE IIIB STAGE IV
  MBD1 MUTATED            0        0
  MBD1 WILD-TYPE         11       25
D328V3, multiclass
            clus
vv           MBD1 MUTATED MBD1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              3            130
  STAGE IIA             1             45
  STAGE IIB             0             67
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MBD1 MUTATED     3   6   1   0
  MBD1 WILD-TYPE 152 255  42  18
D328V4, multiclass
    clus
vv   MBD1 MUTATED MBD1 WILD-TYPE
  T1            3            152
  T2            6            255
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  MBD1 MUTATED     7   1     2
  MBD1 WILD-TYPE 300  88    70
D328V5, multiclass
       clus
vv      MBD1 MUTATED MBD1 WILD-TYPE
  N0               7            300
  N1               1             88
  N2+N3            2             70
[1] 3 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
  MBD1 MUTATED    10   0
  MBD1 WILD-TYPE 317  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED     10    0
  MBD1 WILD-TYPE  317   23
   clus
vv  MBD1 MUTATED MBD1 WILD-TYPE
  0           10            317
  1            0             23
[1] 2 2
[1] FALSE
D328V7, binary
                cls
clus               0   1
  MBD1 MUTATED     4   6
  MBD1 WILD-TYPE 255 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      4    6
  MBD1 WILD-TYPE  255  215
        clus
vv       MBD1 MUTATED MBD1 WILD-TYPE
  FEMALE            4            255
  MALE              6            215
[1] 2 2
[1] FALSE
D328V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MBD1 MUTATED                            0                                 0
  MBD1 WILD-TYPE                         18                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MBD1 MUTATED                                                    9
  MBD1 WILD-TYPE                                                285
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MBD1 MUTATED                                            0
  MBD1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MBD1 MUTATED                                               1
  MBD1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MBD1 MUTATED                                0
  MBD1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MBD1 MUTATED                                    0
  MBD1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MBD1 MUTATED                              0                             0
  MBD1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MBD1 MUTATED                                               0
  MBD1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MBD1 MUTATED                              0
  MBD1 WILD-TYPE                            9
D328V9, multiclass
                                                    clus
vv                                                   MBD1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MBD1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V10, binary
                cls
clus               0   1
  MBD1 MUTATED     0  10
  MBD1 WILD-TYPE  20 450
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      0   10
  MBD1 WILD-TYPE   20  450
     clus
vv    MBD1 MUTATED MBD1 WILD-TYPE
  NO             0             20
  YES           10            450
[1] 2 2
[1] FALSE
D328V11, continuous
D328V12, continuous
                vv
clus              R0  R1  R2  RX
  MBD1 MUTATED     9   0   0   0
  MBD1 WILD-TYPE 301  11   4  25
D328V13, multiclass
    clus
vv   MBD1 MUTATED MBD1 WILD-TYPE
  R0            9            301
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBD1 MUTATED                                  0     0
  MBD1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MBD1 MUTATED                           1     8
  MBD1 WILD-TYPE                        28   369
D328V14, multiclass
                                  clus
vv                                 MBD1 MUTATED MBD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V15, binary
                cls
clus               0   1
  MBD1 MUTATED     0   6
  MBD1 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      0    6
  MBD1 WILD-TYPE    6  343
                        clus
vv                       MBD1 MUTATED MBD1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(329) Variable = WAC MUTATION ANALYSIS
D329V1, survival
               sevent
clus2             0   1
  WAC MUTATED     6   5
  WAC WILD-TYPE 309 136
  WAC MUTATED WAC WILD-TYPE 
           11           445 
  WAC MUTATED WAC WILD-TYPE 
            5           136 
$`WAC MUTATED`
TCGA-05-4389 TCGA-05-4397 TCGA-38-7271 TCGA-44-6146 TCGA-44-7662 TCGA-50-5930 
       45.01        24.03        26.30         9.93         7.17         9.27 
TCGA-55-8614 TCGA-62-A46Y TCGA-86-8073 TCGA-L9-A443 TCGA-MP-A4TI 
       17.62        13.61        24.33         3.81        14.10 

$`WAC WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       12.59        23.77        10.78        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        8.22        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        67.96        72.30        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  WAC MUTATED WAC WILD-TYPE 
         3.81          0.00 
  WAC MUTATED WAC WILD-TYPE 
        45.01        223.96 
  WAC MUTATED WAC WILD-TYPE 
        14.10         18.12 
[1] "3.8 - 45.0 (14.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.2"
D329V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  WAC MUTATED         0        3        3         1         2          2
  WAC WILD-TYPE       4      120      130        45        65         68
               vv
clus            STAGE IIIB STAGE IV
  WAC MUTATED            0        0
  WAC WILD-TYPE         11       25
D329V3, multiclass
            clus
vv           WAC MUTATED WAC WILD-TYPE
  STAGE I              0             4
  STAGE IA             3           120
  STAGE IB             3           130
  STAGE IIA            1            45
  STAGE IIB            2            65
  STAGE IIIA           2            68
  STAGE IIIB           0            11
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  WAC MUTATED     3   7   1   0
  WAC WILD-TYPE 152 254  42  18
D329V4, multiclass
    clus
vv   WAC MUTATED WAC WILD-TYPE
  T1           3           152
  T2           7           254
  T3           1            42
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  WAC MUTATED     7   2     2
  WAC WILD-TYPE 300  87    70
D329V5, multiclass
       clus
vv      WAC MUTATED WAC WILD-TYPE
  N0              7           300
  N1              2            87
  N2+N3           2            70
[1] 3 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
  WAC MUTATED     8   0
  WAC WILD-TYPE 319  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED      8    0
  WAC WILD-TYPE  319   23
   clus
vv  WAC MUTATED WAC WILD-TYPE
  0           8           319
  1           0            23
[1] 2 2
[1] FALSE
D329V7, binary
               cls
clus              0   1
  WAC MUTATED     3   8
  WAC WILD-TYPE 256 213
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED      3    8
  WAC WILD-TYPE  256  213
        clus
vv       WAC MUTATED WAC WILD-TYPE
  FEMALE           3           256
  MALE             8           213
[1] 2 2
[1] FALSE
D329V8, continuous
[1] "Remove cluster labels:" "WAC MUTATED"           
clus
  WAC MUTATED WAC WILD-TYPE 
            1            83 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A470 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681    TCGA-64-5778 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520    TCGA-73-4659 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-86-8279    TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-86-8669    TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
   TCGA-MN-A4N1    TCGA-MN-A4N4    TCGA-MN-A4N5 
"WAC WILD-TYPE" "WAC WILD-TYPE" "WAC WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  WAC MUTATED                            0                                 4
  WAC WILD-TYPE                         18                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  WAC MUTATED                                                    5
  WAC WILD-TYPE                                                289
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  WAC MUTATED                                            0
  WAC WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  WAC MUTATED                                               1
  WAC WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  WAC MUTATED                                0
  WAC WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  WAC MUTATED                                    0                            1
  WAC WILD-TYPE                                  3                            1
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  WAC MUTATED                               0
  WAC WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  WAC MUTATED                                               0
  WAC WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  WAC MUTATED                              0
  WAC WILD-TYPE                            9
D329V9, multiclass
                                                    clus
vv                                                   WAC MUTATED WAC WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           5           289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 1             1
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V10, binary
               cls
clus              0   1
  WAC MUTATED     1  10
  WAC WILD-TYPE  19 450
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED      1   10
  WAC WILD-TYPE   19  450
     clus
vv    WAC MUTATED WAC WILD-TYPE
  NO            1            19
  YES          10           450
[1] 2 2
[1] FALSE
D329V11, continuous
D329V12, continuous
               vv
clus             R0  R1  R2  RX
  WAC MUTATED     8   0   0   0
  WAC WILD-TYPE 302  11   4  25
D329V13, multiclass
    clus
vv   WAC MUTATED WAC WILD-TYPE
  R0           8           302
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WAC MUTATED                                  0     0
  WAC WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  WAC MUTATED                           0     9
  WAC WILD-TYPE                        29   368
D329V14, multiclass
                                  clus
vv                                 WAC MUTATED WAC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                      9           368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V15, binary
               cls
clus              0   1
  WAC MUTATED     0   9
  WAC WILD-TYPE   6 340
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED      0    9
  WAC WILD-TYPE    6  340
                        clus
vv                       WAC MUTATED WAC WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           9           340
[1] 2 2
[1] FALSE

Clustering(330) Variable = PGBD1 MUTATION ANALYSIS
D330V1, survival
                 sevent
clus2               0   1
  PGBD1 MUTATED    10   7
  PGBD1 WILD-TYPE 305 134
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             17             439 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
              7             134 
$`PGBD1 MUTATED`
TCGA-55-6982 TCGA-55-7911 TCGA-55-A490 TCGA-67-6215 TCGA-73-4659 TCGA-73-4676 
       32.71        17.65         1.58         5.72        23.38         5.39 
TCGA-78-7152 TCGA-78-7155 TCGA-78-8660 TCGA-86-7954 TCGA-86-8358 TCGA-86-A4JF 
       39.52        38.50        10.55        19.89        21.47        17.62 
TCGA-95-7039 TCGA-95-7948 TCGA-97-8176 TCGA-MP-A4TA TCGA-MP-A4TF 
        1.12        15.65        15.39        31.23        11.05 

$`PGBD1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       45.34        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.04         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        0.10        52.60        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        1.32         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
        5.69        19.27        20.58        35.93        21.90        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
      214.62        39.75        77.59       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.68        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       18.12        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PGBD1 MUTATED PGBD1 WILD-TYPE 
           1.12            0.00 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
          39.52          223.96 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
          17.62           18.12 
[1] "1.1 - 39.5 (17.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.9"
D330V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PGBD1 MUTATED         0        2        6         3         4          2
  PGBD1 WILD-TYPE       4      121      127        43        63         68
                 vv
clus              STAGE IIIB STAGE IV
  PGBD1 MUTATED            0        0
  PGBD1 WILD-TYPE         11       25
D330V3, multiclass
            clus
vv           PGBD1 MUTATED PGBD1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               6             127
  STAGE IIA              3              43
  STAGE IIB              4              63
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of 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     2  12   3   0
  PGBD1 WILD-TYPE 153 249  40  18
D330V4, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  T1             2             153
  T2            12             249
  T3             3              40
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  PGBD1 MUTATED    12   4     1
  PGBD1 WILD-TYPE 295  85    71
D330V5, multiclass
       clus
vv      PGBD1 MUTATED PGBD1 WILD-TYPE
  N0               12             295
  N1                4              85
  N2+N3             1              71
[1] 3 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
  PGBD1 MUTATED    14   0
  PGBD1 WILD-TYPE 313  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED     14    0
  PGBD1 WILD-TYPE  313   23
   clus
vv  PGBD1 MUTATED PGBD1 WILD-TYPE
  0            14             313
  1             0              23
[1] 2 2
[1] FALSE
D330V7, binary
                 cls
clus                0   1
  PGBD1 MUTATED     8   9
  PGBD1 WILD-TYPE 251 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      8    9
  PGBD1 WILD-TYPE  251  212
        clus
vv       PGBD1 MUTATED PGBD1 WILD-TYPE
  FEMALE             8             251
  MALE               9             212
[1] 2 2
[1] FALSE
D330V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PGBD1 MUTATED                            1                                 3
  PGBD1 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PGBD1 MUTATED                                                   12
  PGBD1 WILD-TYPE                                                282
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PGBD1 MUTATED                                            0
  PGBD1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PGBD1 MUTATED                                               1
  PGBD1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PGBD1 MUTATED                                0
  PGBD1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PGBD1 MUTATED                                    0
  PGBD1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PGBD1 MUTATED                              0                             0
  PGBD1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PGBD1 MUTATED                                               0
  PGBD1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PGBD1 MUTATED                              0
  PGBD1 WILD-TYPE                            9
D330V9, multiclass
                                                    clus
vv                                                   PGBD1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PGBD1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V10, binary
                 cls
clus                0   1
  PGBD1 MUTATED     1  16
  PGBD1 WILD-TYPE  19 444
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      1   16
  PGBD1 WILD-TYPE   19  444
     clus
vv    PGBD1 MUTATED PGBD1 WILD-TYPE
  NO              1              19
  YES            16             444
[1] 2 2
[1] FALSE
D330V11, continuous
D330V12, continuous
                 vv
clus               R0  R1  R2  RX
  PGBD1 MUTATED    15   0   0   0
  PGBD1 WILD-TYPE 295  11   4  25
D330V13, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  R0            15             295
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PGBD1 MUTATED                                  0     0
  PGBD1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PGBD1 MUTATED                           0    16
  PGBD1 WILD-TYPE                        29   361
D330V14, multiclass
                                  clus
vv                                 PGBD1 MUTATED PGBD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       16             361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V15, binary
                 cls
clus                0   1
  PGBD1 MUTATED     0  13
  PGBD1 WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      0   13
  PGBD1 WILD-TYPE    6  336
                        clus
vv                       PGBD1 MUTATED PGBD1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(331) Variable = GRHL2 MUTATION ANALYSIS
D331V1, survival
                 sevent
clus2               0   1
  GRHL2 MUTATED     7   2
  GRHL2 WILD-TYPE 308 139
  GRHL2 MUTATED GRHL2 WILD-TYPE 
              9             447 
  GRHL2 MUTATED GRHL2 WILD-TYPE 
              2             139 
$`GRHL2 MUTATED`
TCGA-05-5425 TCGA-38-4632 TCGA-55-7994 TCGA-55-8619 TCGA-55-A48Y TCGA-62-A471 
       29.00        44.61        19.82         1.61        20.71        40.96 
TCGA-69-7973 TCGA-78-7154 TCGA-95-7043 
        7.56        19.50         1.22 

$`GRHL2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 
        1.58         2.17        16.93        22.65        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       13.61        39.25        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  GRHL2 MUTATED GRHL2 WILD-TYPE 
           1.22            0.00 
  GRHL2 MUTATED GRHL2 WILD-TYPE 
          44.61          223.96 
  GRHL2 MUTATED GRHL2 WILD-TYPE 
          19.82           17.92 
[1] "1.2 - 44.6 (19.8)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.2"
D331V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GRHL2 MUTATED         0        1        1         1         4          1
  GRHL2 WILD-TYPE       4      122      132        45        63         69
                 vv
clus              STAGE IIIB STAGE IV
  GRHL2 MUTATED            0        1
  GRHL2 WILD-TYPE         11       24
D331V3, multiclass
            clus
vv           GRHL2 MUTATED GRHL2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               1             132
  STAGE IIA              1              45
  STAGE IIB              4              63
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRHL2 MUTATED     1   5   3   0
  GRHL2 WILD-TYPE 154 256  40  18
D331V4, multiclass
    clus
vv   GRHL2 MUTATED GRHL2 WILD-TYPE
  T1             1             154
  T2             5             256
  T3             3              40
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  GRHL2 MUTATED     5   3     1
  GRHL2 WILD-TYPE 302  86    71
D331V5, multiclass
       clus
vv      GRHL2 MUTATED GRHL2 WILD-TYPE
  N0                5             302
  N1                3              86
  N2+N3             1              71
[1] 3 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
  GRHL2 MUTATED     5   1
  GRHL2 WILD-TYPE 322  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHL2 MUTATED      5    1
  GRHL2 WILD-TYPE  322   22
   clus
vv  GRHL2 MUTATED GRHL2 WILD-TYPE
  0             5             322
  1             1              22
[1] 2 2
[1] FALSE
D331V7, binary
                 cls
clus                0   1
  GRHL2 MUTATED     3   6
  GRHL2 WILD-TYPE 256 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHL2 MUTATED      3    6
  GRHL2 WILD-TYPE  256  215
        clus
vv       GRHL2 MUTATED GRHL2 WILD-TYPE
  FEMALE             3             256
  MALE               6             215
[1] 2 2
[1] FALSE
D331V8, continuous
[1] "Remove cluster labels:" "GRHL2 MUTATED"         
clus
  GRHL2 MUTATED GRHL2 WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A472 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"GRHL2 WILD-TYPE" "GRHL2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GRHL2 MUTATED                            0                                 3
  GRHL2 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GRHL2 MUTATED                                                    5
  GRHL2 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GRHL2 MUTATED                                            0
  GRHL2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GRHL2 MUTATED                                               0
  GRHL2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  GRHL2 MUTATED                                0
  GRHL2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  GRHL2 MUTATED                                    0
  GRHL2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GRHL2 MUTATED                              0                             0
  GRHL2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GRHL2 MUTATED                                               0
  GRHL2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  GRHL2 MUTATED                              1
  GRHL2 WILD-TYPE                            8
D331V9, multiclass
                                                    clus
vv                                                   GRHL2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   GRHL2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V10, binary
                 cls
clus                0   1
  GRHL2 MUTATED     0   9
  GRHL2 WILD-TYPE  20 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHL2 MUTATED      0    9
  GRHL2 WILD-TYPE   20  451
     clus
vv    GRHL2 MUTATED GRHL2 WILD-TYPE
  NO              0              20
  YES             9             451
[1] 2 2
[1] FALSE
D331V11, continuous
D331V12, continuous
                 vv
clus               R0  R1  R2  RX
  GRHL2 MUTATED     7   0   0   0
  GRHL2 WILD-TYPE 303  11   4  25
D331V13, multiclass
    clus
vv   GRHL2 MUTATED GRHL2 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRHL2 MUTATED                                  0     0
  GRHL2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRHL2 MUTATED                           1     7
  GRHL2 WILD-TYPE                        28   370
D331V14, multiclass
                                  clus
vv                                 GRHL2 MUTATED GRHL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V15, binary
                 cls
clus                0   1
  GRHL2 MUTATED     0   7
  GRHL2 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHL2 MUTATED      0    7
  GRHL2 WILD-TYPE    6  342
                        clus
vv                       GRHL2 MUTATED GRHL2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(332) Variable = TARS2 MUTATION ANALYSIS
D332V1, survival
                 sevent
clus2               0   1
  TARS2 MUTATED     5   3
  TARS2 WILD-TYPE 310 138
  TARS2 MUTATED TARS2 WILD-TYPE 
              8             448 
  TARS2 MUTATED TARS2 WILD-TYPE 
              3             138 
$`TARS2 MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-44-4112 TCGA-50-6594 TCGA-55-7574 TCGA-67-3771 
        3.98        45.01        26.56        12.16         3.12        20.05 
TCGA-91-6836 TCGA-93-A4JQ 
       13.71        17.29 

$`TARS2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07        19.96        14.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24        34.06         6.25        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  TARS2 MUTATED TARS2 WILD-TYPE 
           3.12            0.00 
  TARS2 MUTATED TARS2 WILD-TYPE 
          45.01          223.96 
  TARS2 MUTATED TARS2 WILD-TYPE 
           15.5            18.1 
[1] "3.1 - 45.0 (15.5)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.7"
D332V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TARS2 MUTATED         0        3        4         0         1          2
  TARS2 WILD-TYPE       4      120      129        46        66         68
                 vv
clus              STAGE IIIB STAGE IV
  TARS2 MUTATED            0        0
  TARS2 WILD-TYPE         11       25
D332V3, multiclass
            clus
vv           TARS2 MUTATED TARS2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TARS2 MUTATED     3   5   2   0
  TARS2 WILD-TYPE 152 256  41  18
D332V4, multiclass
    clus
vv   TARS2 MUTATED TARS2 WILD-TYPE
  T1             3             152
  T2             5             256
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  TARS2 MUTATED     7   2     1
  TARS2 WILD-TYPE 300  87    71
D332V5, multiclass
       clus
vv      TARS2 MUTATED TARS2 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             1              71
[1] 3 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
  TARS2 MUTATED     8   0
  TARS2 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TARS2 MUTATED      8    0
  TARS2 WILD-TYPE  319   23
   clus
vv  TARS2 MUTATED TARS2 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D332V7, binary
                 cls
clus                0   1
  TARS2 MUTATED     7   3
  TARS2 WILD-TYPE 252 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TARS2 MUTATED      7    3
  TARS2 WILD-TYPE  252  218
        clus
vv       TARS2 MUTATED TARS2 WILD-TYPE
  FEMALE             7             252
  MALE               3             218
[1] 2 2
[1] FALSE
D332V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TARS2 MUTATED                            1                                 2
  TARS2 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TARS2 MUTATED                                                    7
  TARS2 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TARS2 MUTATED                                            0
  TARS2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TARS2 MUTATED                                               0
  TARS2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TARS2 MUTATED                                0
  TARS2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TARS2 MUTATED                                    0
  TARS2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TARS2 MUTATED                              0                             0
  TARS2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TARS2 MUTATED                                               0
  TARS2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TARS2 MUTATED                              0
  TARS2 WILD-TYPE                            9
D332V9, multiclass
                                                    clus
vv                                                   TARS2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   TARS2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V10, binary
                 cls
clus                0   1
  TARS2 MUTATED     1   9
  TARS2 WILD-TYPE  19 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TARS2 MUTATED      1    9
  TARS2 WILD-TYPE   19  451
     clus
vv    TARS2 MUTATED TARS2 WILD-TYPE
  NO              1              19
  YES             9             451
[1] 2 2
[1] FALSE
D332V11, continuous
D332V12, continuous
                 vv
clus               R0  R1  R2  RX
  TARS2 MUTATED     4   1   1   2
  TARS2 WILD-TYPE 306  10   3  23
D332V13, multiclass
    clus
vv   TARS2 MUTATED TARS2 WILD-TYPE
  R0             4             306
  R1             1              10
  R2             1               3
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TARS2 MUTATED                                  0     0
  TARS2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TARS2 MUTATED                           2     4
  TARS2 WILD-TYPE                        27   373
D332V14, multiclass
                                  clus
vv                                 TARS2 MUTATED TARS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V15, binary
                 cls
clus                0   1
  TARS2 MUTATED     0   6
  TARS2 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TARS2 MUTATED      0    6
  TARS2 WILD-TYPE    6  343
                        clus
vv                       TARS2 MUTATED TARS2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(333) Variable = ARHGEF10L MUTATION ANALYSIS
D333V1, survival
                     sevent
clus2                   0   1
  ARHGEF10L MUTATED     6   1
  ARHGEF10L WILD-TYPE 309 140
  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE 
                  7                 449 
  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE 
                  1                 140 
$`ARHGEF10L MUTATED`
TCGA-44-3398 TCGA-44-6775 TCGA-50-6593 TCGA-86-8073 TCGA-91-6848 TCGA-95-7039 
       38.24        23.18        11.05        24.33         7.36         1.12 
TCGA-95-A4VK 
       21.40 

$`ARHGEF10L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        21.63        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE 
               1.12                0.00 
  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE 
              38.24              223.96 
  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE 
              21.40               17.98 
[1] "1.1 - 38.2 (21.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.5"
D333V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARHGEF10L MUTATED         0        1        2         0         1          3
  ARHGEF10L WILD-TYPE       4      122      131        46        66         67
                     vv
clus                  STAGE IIIB STAGE IV
  ARHGEF10L MUTATED            0        1
  ARHGEF10L WILD-TYPE         11       24
D333V3, multiclass
            clus
vv           ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  STAGE I                    0                   4
  STAGE IA                   1                 122
  STAGE IB                   2                 131
  STAGE IIA                  0                  46
  STAGE IIB                  1                  66
  STAGE IIIA                 3                  67
  STAGE IIIB                 0                  11
  STAGE IV                   1                  24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  ARHGEF10L MUTATED     2   5   1   0
  ARHGEF10L WILD-TYPE 153 256  42  18
D333V4, multiclass
    clus
vv   ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  T1                 2                 153
  T2                 5                 256
  T3                 1                  42
  T4                 0                  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"
                     vv
clus                   N0  N1 N2+N3
  ARHGEF10L MUTATED     4   0     4
  ARHGEF10L WILD-TYPE 303  89    68
D333V5, multiclass
       clus
vv      ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  N0                    4                 303
  N1                    0                  89
  N2+N3                 4                  68
[1] 3 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
  ARHGEF10L MUTATED     4   1
  ARHGEF10L WILD-TYPE 323  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGEF10L MUTATED      4    1
  ARHGEF10L WILD-TYPE  323   22
   clus
vv  ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  0                 4                 323
  1                 1                  22
[1] 2 2
[1] FALSE
D333V7, binary
                     cls
clus                    0   1
  ARHGEF10L MUTATED     5   3
  ARHGEF10L WILD-TYPE 254 218
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGEF10L MUTATED      5    3
  ARHGEF10L WILD-TYPE  254  218
        clus
vv       ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  FEMALE                 5                 254
  MALE                   3                 218
[1] 2 2
[1] FALSE
D333V8, continuous
                     vv
clus                  LUNG ACINAR ADENOCARCINOMA
  ARHGEF10L MUTATED                            0
  ARHGEF10L WILD-TYPE                         18
                     vv
clus                  LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARHGEF10L MUTATED                                   3
  ARHGEF10L WILD-TYPE                                99
                     vv
clus                  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF10L MUTATED                                                    4
  ARHGEF10L WILD-TYPE                                                290
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARHGEF10L MUTATED                                            0
  ARHGEF10L WILD-TYPE                                          4
                     vv
clus                  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARHGEF10L MUTATED                                               1
  ARHGEF10L WILD-TYPE                                            18
                     vv
clus                  LUNG CLEAR CELL ADENOCARCINOMA
  ARHGEF10L MUTATED                                0
  ARHGEF10L WILD-TYPE                              2
                     vv
clus                  LUNG MICROPAPILLARY ADENOCARCINOMA
  ARHGEF10L MUTATED                                    0
  ARHGEF10L WILD-TYPE                                  3
                     vv
clus                  LUNG MUCINOUS ADENOCARCINOMA
  ARHGEF10L MUTATED                              0
  ARHGEF10L WILD-TYPE                            2
                     vv
clus                  LUNG PAPILLARY ADENOCARCINOMA
  ARHGEF10L MUTATED                               0
  ARHGEF10L WILD-TYPE                            22
                     vv
clus                  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARHGEF10L MUTATED                                               0
  ARHGEF10L WILD-TYPE                                             5
                     vv
clus                  MUCINOUS (COLLOID) CARCINOMA
  ARHGEF10L MUTATED                              0
  ARHGEF10L WILD-TYPE                            9
D333V9, multiclass
                                                    clus
vv                                                   ARHGEF10L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                         0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      1
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       0
  LUNG PAPILLARY ADENOCARCINOMA                                      0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      0
  MUCINOUS (COLLOID) CARCINOMA                                       0
                                                    clus
vv                                                   ARHGEF10L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                   99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                 290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                           4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                       18
  LUNG CLEAR CELL ADENOCARCINOMA                                       2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                   3
  LUNG MUCINOUS ADENOCARCINOMA                                         2
  LUNG PAPILLARY ADENOCARCINOMA                                       22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                        5
  MUCINOUS (COLLOID) CARCINOMA                                         9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V10, binary
                     cls
clus                    0   1
  ARHGEF10L MUTATED     0   8
  ARHGEF10L WILD-TYPE  20 452
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGEF10L MUTATED      0    8
  ARHGEF10L WILD-TYPE   20  452
     clus
vv    ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  NO                  0                  20
  YES                 8                 452
[1] 2 2
[1] FALSE
D333V11, continuous
D333V12, continuous
                     vv
clus                   R0  R1  R2  RX
  ARHGEF10L MUTATED     3   0   0   3
  ARHGEF10L WILD-TYPE 307  11   4  22
D333V13, multiclass
    clus
vv   ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  R0                 3                 307
  R1                 0                  11
  R2                 0                   4
  RX                 3                  22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF10L MUTATED                                  0     0
  ARHGEF10L WILD-TYPE                                1     7
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF10L MUTATED                           0     7
  ARHGEF10L WILD-TYPE                        29   370
D333V14, multiclass
                                  clus
vv                                 ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                   7
  BLACK OR AFRICAN AMERICAN                        0                  29
  WHITE                                            7                 370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V15, binary
                     cls
clus                    0   1
  ARHGEF10L MUTATED     1   6
  ARHGEF10L WILD-TYPE   5 343
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGEF10L MUTATED      1    6
  ARHGEF10L WILD-TYPE    5  343
                        clus
vv                       ARHGEF10L MUTATED ARHGEF10L WILD-TYPE
  HISPANIC OR LATINO                     1                   5
  NOT HISPANIC OR LATINO                 6                 343
[1] 2 2
[1] FALSE

Clustering(334) Variable = EIF4G3 MUTATION ANALYSIS
D334V1, survival
                  sevent
clus2                0   1
  EIF4G3 MUTATED     9   2
  EIF4G3 WILD-TYPE 306 139
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              11              445 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
               2              139 
$`EIF4G3 MUTATED`
TCGA-05-4382 TCGA-44-5644 TCGA-55-7907 TCGA-55-7910 TCGA-55-8511 TCGA-55-8621 
       19.96        28.37         0.53         6.48         0.30        16.93 
TCGA-73-4670 TCGA-78-7150 TCGA-78-7156 TCGA-78-8640 TCGA-86-7955 
        4.31        21.90        32.09       214.62        16.70 

$`EIF4G3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.78         1.45        18.64        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
        0.95         0.36         0.26         0.49        17.72         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       23.38        29.98        26.30        15.35         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58        35.93        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
             0.3              0.0 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
          214.62           223.96 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
           16.93            18.08 
[1] "0.3 - 214.6 (16.9)" "0.0 - 224.0 (18.1)"
[1] "hr=" "2"  
D334V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  EIF4G3 MUTATED         0        1        5         3         1          1
  EIF4G3 WILD-TYPE       4      122      128        43        66         69
                  vv
clus               STAGE IIIB STAGE IV
  EIF4G3 MUTATED            0        2
  EIF4G3 WILD-TYPE         11       23
D334V3, multiclass
            clus
vv           EIF4G3 MUTATED EIF4G3 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                5              128
  STAGE IIA               3               43
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   9   1   1
  EIF4G3 WILD-TYPE 153 252  42  17
D334V4, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  T1              2              153
  T2              9              252
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  EIF4G3 MUTATED     8   4     1
  EIF4G3 WILD-TYPE 299  85    71
D334V5, multiclass
       clus
vv      EIF4G3 MUTATED EIF4G3 WILD-TYPE
  N0                 8              299
  N1                 4               85
  N2+N3              1               71
[1] 3 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
  EIF4G3 MUTATED     7   2
  EIF4G3 WILD-TYPE 320  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      7    2
  EIF4G3 WILD-TYPE  320   21
   clus
vv  EIF4G3 MUTATED EIF4G3 WILD-TYPE
  0              7              320
  1              2               21
[1] 2 2
[1] FALSE
D334V7, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED     6   7
  EIF4G3 WILD-TYPE 253 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      6    7
  EIF4G3 WILD-TYPE  253  214
        clus
vv       EIF4G3 MUTATED EIF4G3 WILD-TYPE
  FEMALE              6              253
  MALE                7              214
[1] 2 2
[1] FALSE
D334V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EIF4G3 MUTATED                            0                                 2
  EIF4G3 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EIF4G3 MUTATED                                                   10
  EIF4G3 WILD-TYPE                                                284
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  EIF4G3 MUTATED                                            0
  EIF4G3 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  EIF4G3 MUTATED                                               0
  EIF4G3 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  EIF4G3 MUTATED                                0
  EIF4G3 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  EIF4G3 MUTATED                                    0
  EIF4G3 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  EIF4G3 MUTATED                              0                             1
  EIF4G3 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  EIF4G3 MUTATED                                               0
  EIF4G3 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  EIF4G3 MUTATED                              0
  EIF4G3 WILD-TYPE                            9
D334V9, multiclass
                                                    clus
vv                                                   EIF4G3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   EIF4G3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V10, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED     0  13
  EIF4G3 WILD-TYPE  20 447
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      0   13
  EIF4G3 WILD-TYPE   20  447
     clus
vv    EIF4G3 MUTATED EIF4G3 WILD-TYPE
  NO               0               20
  YES             13              447
[1] 2 2
[1] FALSE
D334V11, continuous
D334V12, continuous
                  vv
clus                R0  R1  R2  RX
  EIF4G3 MUTATED    10   0   1   1
  EIF4G3 WILD-TYPE 300  11   3  24
D334V13, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  R0             10              300
  R1              0               11
  R2              1                3
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF4G3 MUTATED                                  0     0
  EIF4G3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF4G3 MUTATED                           1     8
  EIF4G3 WILD-TYPE                        28   369
D334V14, multiclass
                                  clus
vv                                 EIF4G3 MUTATED EIF4G3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         8              369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V15, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED     0   7
  EIF4G3 WILD-TYPE   6 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      0    7
  EIF4G3 WILD-TYPE    6  342
                        clus
vv                       EIF4G3 MUTATED EIF4G3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(335) Variable = CRTC3 MUTATION ANALYSIS
D335V1, survival
                 sevent
clus2               0   1
  CRTC3 MUTATED     1   1
  CRTC3 WILD-TYPE 314 140
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              2             454 
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              1             140 
$`CRTC3 MUTATED`
TCGA-05-4389 TCGA-50-5930 
       45.01         9.27 

$`CRTC3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  CRTC3 MUTATED CRTC3 WILD-TYPE 
           9.27            0.00 
  CRTC3 MUTATED CRTC3 WILD-TYPE 
          45.01          223.96 
  CRTC3 MUTATED CRTC3 WILD-TYPE 
          27.14           18.03 
[1] "9.3 - 45.0 (27.1)"  "0.0 - 224.0 (18.0)"
[1] "Remove cluster labels:" "CRTC3 MUTATED"         
D335V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CRTC3 MUTATED         0        1        1         0         0          1
  CRTC3 WILD-TYPE       4      122      132        46        67         69
                 vv
clus              STAGE IIIB STAGE IV
  CRTC3 MUTATED            0        0
  CRTC3 WILD-TYPE         11       25
D335V3, multiclass
            clus
vv           CRTC3 MUTATED CRTC3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               1             132
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRTC3 MUTATED     1   2   0   0
  CRTC3 WILD-TYPE 154 259  43  18
D335V4, multiclass
    clus
vv   CRTC3 MUTATED CRTC3 WILD-TYPE
  T1             1             154
  T2             2             259
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  CRTC3 MUTATED     2   0     1
  CRTC3 WILD-TYPE 305  89    71
D335V5, multiclass
       clus
vv      CRTC3 MUTATED CRTC3 WILD-TYPE
  N0                2             305
  N1                0              89
  N2+N3             1              71
[1] 3 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
  CRTC3 MUTATED     3   0
  CRTC3 WILD-TYPE 324  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC3 MUTATED      3    0
  CRTC3 WILD-TYPE  324   23
   clus
vv  CRTC3 MUTATED CRTC3 WILD-TYPE
  0             3             324
  1             0              23
[1] 2 2
[1] FALSE
D335V7, binary
                 cls
clus                0   1
  CRTC3 MUTATED     0   3
  CRTC3 WILD-TYPE 259 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC3 MUTATED      0    3
  CRTC3 WILD-TYPE  259  218
        clus
vv       CRTC3 MUTATED CRTC3 WILD-TYPE
  FEMALE             0             259
  MALE               3             218
[1] 2 2
[1] FALSE
D335V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CRTC3 MUTATED                            0                                 3
  CRTC3 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CRTC3 MUTATED                                                    0
  CRTC3 WILD-TYPE                                                294
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CRTC3 MUTATED                                            0
  CRTC3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CRTC3 MUTATED                                               0
  CRTC3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CRTC3 MUTATED                                0
  CRTC3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CRTC3 MUTATED                                    0
  CRTC3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CRTC3 MUTATED                              0                             0
  CRTC3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CRTC3 MUTATED                                               0
  CRTC3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CRTC3 MUTATED                              0
  CRTC3 WILD-TYPE                            9
D335V9, multiclass
                                                    clus
vv                                                   CRTC3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CRTC3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             294
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V10, binary
                 cls
clus                0   1
  CRTC3 MUTATED     1   2
  CRTC3 WILD-TYPE  19 458
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC3 MUTATED      1    2
  CRTC3 WILD-TYPE   19  458
     clus
vv    CRTC3 MUTATED CRTC3 WILD-TYPE
  NO              1              19
  YES             2             458
[1] 2 2
[1] FALSE
D335V11, continuous
[1] "Remove cluster labels:" "CRTC3 MUTATED"         
clus
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              2             331 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4397 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4398      TCGA-05-4405      TCGA-05-4415      TCGA-05-4417 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4418      TCGA-05-4420      TCGA-05-4422      TCGA-05-4424 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4425      TCGA-05-4426      TCGA-05-4427      TCGA-05-4430 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4432      TCGA-05-4433      TCGA-05-4434      TCGA-05-5420 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-5423      TCGA-05-5425      TCGA-05-5428      TCGA-35-4122 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-35-4123      TCGA-35-5375      TCGA-38-4625      TCGA-38-4626 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-4629      TCGA-38-4631      TCGA-38-4632      TCGA-38-7271 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5643 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-5644      TCGA-44-5645      TCGA-44-6144      TCGA-44-6145 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6146      TCGA-44-6148      TCGA-44-6774      TCGA-44-6775 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6776      TCGA-44-6777      TCGA-44-6778      TCGA-44-6779 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-7659      TCGA-44-7660      TCGA-44-7661      TCGA-44-7662 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-7667      TCGA-44-7669      TCGA-44-7670      TCGA-44-7672 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-8117      TCGA-44-8119      TCGA-44-8120      TCGA-44-A479 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-A4SS      TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4487 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4490      TCGA-49-4494      TCGA-49-4505      TCGA-49-4506 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4507      TCGA-49-4510      TCGA-49-4514      TCGA-49-6742 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-6743      TCGA-49-6744      TCGA-49-6745      TCGA-49-6761 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-6767      TCGA-50-5051      TCGA-50-5072      TCGA-50-5931 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-5939      TCGA-50-5941      TCGA-50-5942      TCGA-50-6590 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-7109      TCGA-50-8457      TCGA-50-8459      TCGA-53-7624 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ      TCGA-55-6543 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6971      TCGA-55-6983      TCGA-55-6985      TCGA-55-7281 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7574      TCGA-55-7724      TCGA-55-7725 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7726      TCGA-55-7728      TCGA-55-7903      TCGA-55-7907 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-7994 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7995      TCGA-55-8089      TCGA-55-8092      TCGA-55-8094 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8096      TCGA-55-8097      TCGA-55-8203      TCGA-55-8205 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8511      TCGA-55-8512      TCGA-55-8514 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8614      TCGA-55-8615      TCGA-55-8620      TCGA-55-8621 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A491      TCGA-55-A492      TCGA-55-A493      TCGA-55-A494 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A4DF      TCGA-55-A4DG      TCGA-62-8398      TCGA-62-8399 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-A470      TCGA-62-A471      TCGA-62-A472      TCGA-64-1676 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1679      TCGA-64-5774      TCGA-64-5775 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-5778      TCGA-64-5779      TCGA-64-5781      TCGA-64-5815 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-7761      TCGA-69-7763      TCGA-69-7764      TCGA-69-7973 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7978      TCGA-69-7979      TCGA-69-7980 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-8253      TCGA-69-8254      TCGA-69-8255      TCGA-69-A59K 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4658      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4675      TCGA-73-4676 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-7498      TCGA-75-5122      TCGA-75-5125      TCGA-75-5126 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-75-6203      TCGA-75-6206      TCGA-75-6207      TCGA-75-6211 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7027      TCGA-75-7031      TCGA-78-7145 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7146      TCGA-78-7147      TCGA-78-7148      TCGA-78-7149 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7150      TCGA-78-7152      TCGA-78-7153      TCGA-78-7154 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7155      TCGA-78-7156      TCGA-78-7158      TCGA-78-7159 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7160      TCGA-78-7161      TCGA-78-7162      TCGA-78-7163 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7166      TCGA-78-7167      TCGA-78-7220      TCGA-78-7535 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7536      TCGA-78-7537      TCGA-78-7539      TCGA-78-7542 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7633      TCGA-78-8640      TCGA-78-8648      TCGA-78-8655 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-8660      TCGA-78-8662      TCGA-80-5607      TCGA-80-5608 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-80-5611      TCGA-83-5908      TCGA-86-6851      TCGA-86-7701 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7714      TCGA-86-7954      TCGA-86-8054 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8358      TCGA-86-8359      TCGA-86-8669 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8673      TCGA-86-8674      TCGA-91-6829      TCGA-91-6830 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-6835      TCGA-91-6836      TCGA-91-6840      TCGA-91-6849 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-7771      TCGA-91-8499      TCGA-91-A4BC      TCGA-93-7347 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-7039      TCGA-95-7043      TCGA-95-7562      TCGA-95-7944 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-7947      TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547      TCGA-97-7552 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7937      TCGA-97-7938 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-7941      TCGA-97-8171      TCGA-97-8172      TCGA-97-8174 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-8176      TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-A4M1      TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025      TCGA-99-8028 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-99-8032      TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-L4-A4E5      TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY      TCGA-MP-A4T2 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7      TCGA-MP-A4T8 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TD 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YF      TCGA-NJ-A4YG 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ      TCGA-NJ-A55A 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
D335V12, continuous
[1] "Remove cluster labels:" "CRTC3 MUTATED"         
clus
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              1             256 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4415      TCGA-05-4417      TCGA-05-4424      TCGA-05-4427 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4433      TCGA-05-5420      TCGA-05-5423      TCGA-05-5425 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-5428      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-4625      TCGA-38-4626      TCGA-38-7271      TCGA-38-A44F 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-2656      TCGA-44-2657      TCGA-44-3396      TCGA-44-3398 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-5644      TCGA-44-5645 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6145      TCGA-44-6147      TCGA-44-6148 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6774      TCGA-44-6775      TCGA-44-6776      TCGA-44-6777 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6778      TCGA-44-6779      TCGA-44-7659      TCGA-44-7660 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-7661      TCGA-44-7662      TCGA-44-7667      TCGA-44-7669 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-7670      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4494      TCGA-49-4505      TCGA-53-7624 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ      TCGA-55-1592 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-1595      TCGA-55-5899      TCGA-55-6642      TCGA-55-6712 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6971      TCGA-55-7227      TCGA-55-7283      TCGA-55-7570 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7576      TCGA-55-7724      TCGA-55-7725 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7726      TCGA-55-7728      TCGA-55-7907      TCGA-55-7910 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7911      TCGA-55-7914      TCGA-55-8089      TCGA-55-8092 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8094      TCGA-55-8096      TCGA-55-8097      TCGA-55-8205 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8299      TCGA-55-8301      TCGA-55-8302      TCGA-55-8506 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8511      TCGA-55-8512      TCGA-55-8514 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8615      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-62-8398 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5774      TCGA-64-5775 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-5778      TCGA-64-5779      TCGA-64-5781      TCGA-69-7761 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-7763      TCGA-69-7764      TCGA-69-7765      TCGA-69-7974 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-7979      TCGA-69-8253      TCGA-69-8255      TCGA-69-A59K 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4670      TCGA-73-4675      TCGA-73-4676      TCGA-73-7498 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7031 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-80-5608      TCGA-83-5908      TCGA-86-6851      TCGA-86-7711 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-8054      TCGA-86-8055 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8281 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8673 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-91-6829      TCGA-91-6830 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7567      TCGA-95-7944      TCGA-95-7947 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8176 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A5C7      TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  CRTC3 MUTATED     1   0   0   1
  CRTC3 WILD-TYPE 309  11   4  24
D335V13, multiclass
[1] "Remove cluster labels:" "CRTC3 MUTATED"         
clus
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              2             348 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4395      TCGA-05-4396 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4397      TCGA-05-4398      TCGA-05-4402      TCGA-05-4403 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4405      TCGA-05-4415      TCGA-05-4417      TCGA-05-4418 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4420      TCGA-05-4422      TCGA-05-4424      TCGA-05-4425 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4426      TCGA-05-4427      TCGA-05-4430      TCGA-05-4432 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-4433      TCGA-05-4434      TCGA-05-5420      TCGA-05-5423 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-05-5429      TCGA-05-5715 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-38-4625 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-4626      TCGA-38-4627      TCGA-38-4628      TCGA-38-4629 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-4630      TCGA-38-4631      TCGA-38-4632      TCGA-38-6178 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-7271      TCGA-38-A44F      TCGA-44-2657      TCGA-44-2661 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-2665      TCGA-44-3396      TCGA-44-3398      TCGA-44-3918 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-3919      TCGA-44-4112      TCGA-44-6144      TCGA-44-6148 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-A47G      TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4487 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4488      TCGA-49-4494      TCGA-49-4501      TCGA-49-4505 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4506      TCGA-49-4507      TCGA-49-4510      TCGA-49-4512 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4514      TCGA-49-6742      TCGA-49-6744      TCGA-49-6761 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-6767      TCGA-50-5051      TCGA-50-5055      TCGA-50-5066 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-5931      TCGA-50-5942      TCGA-50-5944      TCGA-50-6593 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-6597      TCGA-50-6673      TCGA-50-8460      TCGA-53-7624 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-53-7626      TCGA-53-A4EZ      TCGA-55-1592      TCGA-55-5899 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6642      TCGA-55-6970      TCGA-55-6971      TCGA-55-6972 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6980      TCGA-55-6981      TCGA-55-6983      TCGA-55-6985 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7281      TCGA-55-7284      TCGA-55-7570      TCGA-55-7574 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7576      TCGA-55-7724      TCGA-55-7725      TCGA-55-7726 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7727      TCGA-55-7728      TCGA-55-7815      TCGA-55-7903 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7907      TCGA-55-7910      TCGA-55-7911      TCGA-55-7914 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7994      TCGA-55-7995      TCGA-55-8085      TCGA-55-8087 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8090      TCGA-55-8091      TCGA-55-8092 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8094      TCGA-55-8097      TCGA-55-8203      TCGA-55-8204 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8206      TCGA-55-8207      TCGA-55-8208 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8299      TCGA-55-8301      TCGA-55-8302      TCGA-55-8505 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8506      TCGA-55-8507      TCGA-55-8508      TCGA-55-8510 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8513      TCGA-55-8514 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8614      TCGA-55-8615      TCGA-55-8616      TCGA-55-8619 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-1676      TCGA-64-1677      TCGA-64-1679      TCGA-64-1681 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-5774      TCGA-64-5775      TCGA-64-5778      TCGA-64-5779 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-5781      TCGA-64-5815      TCGA-67-3771      TCGA-67-3773 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-67-4679      TCGA-67-6215      TCGA-67-6216      TCGA-67-6217 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4658      TCGA-73-4659 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-4677      TCGA-73-7498 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-7499      TCGA-75-5122      TCGA-75-5125      TCGA-75-5126 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-75-5146      TCGA-75-5147      TCGA-75-6203      TCGA-75-6205 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-75-6206      TCGA-75-6207      TCGA-75-6211      TCGA-75-6212 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7030 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7143      TCGA-78-7145      TCGA-78-7146 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7147      TCGA-78-7148      TCGA-78-7149      TCGA-78-7150 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7152      TCGA-78-7153      TCGA-78-7154      TCGA-78-7155 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7156      TCGA-78-7158      TCGA-78-7159      TCGA-78-7160 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7161      TCGA-78-7162      TCGA-78-7163      TCGA-78-7166 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7167      TCGA-78-7220      TCGA-78-7535      TCGA-78-7536 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7537      TCGA-78-7539      TCGA-78-7540      TCGA-78-7542 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7633      TCGA-78-8640      TCGA-78-8648      TCGA-78-8655 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-8660      TCGA-78-8662      TCGA-80-5607      TCGA-80-5608 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-80-5611      TCGA-83-5908      TCGA-86-6562      TCGA-86-7701 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7713      TCGA-86-7714      TCGA-86-7953 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8054      TCGA-86-8055 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8075 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8585      TCGA-86-8668 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8671      TCGA-86-8672      TCGA-86-8673 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-6828      TCGA-91-6829      TCGA-91-6835      TCGA-91-6840 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-A4BD      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JP      TCGA-93-A4JQ 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-8039      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-97-7546 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-7554      TCGA-97-7938      TCGA-97-7941      TCGA-97-8176 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-99-8028      TCGA-99-8032      TCGA-99-8033      TCGA-J2-A4AD 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-J2-A4AE      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4T8      TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YQ 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRTC3 MUTATED                                  0     0
  CRTC3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CRTC3 MUTATED                           0     1
  CRTC3 WILD-TYPE                        29   376
D335V14, multiclass
[1] "Remove cluster labels:" "CRTC3 MUTATED"         
clus
  CRTC3 MUTATED CRTC3 WILD-TYPE 
              1             413 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-38-4625 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-4626      TCGA-38-4627      TCGA-38-4628      TCGA-38-4629 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-4630      TCGA-38-4631      TCGA-38-4632      TCGA-38-6178 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-2661      TCGA-44-2665      TCGA-44-3396      TCGA-44-3398 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-3919      TCGA-44-4112      TCGA-44-5643 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-5644      TCGA-44-5645      TCGA-44-6144      TCGA-44-6145 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6146      TCGA-44-6147      TCGA-44-6148      TCGA-44-6774 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-6776      TCGA-44-6777      TCGA-44-6778 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-6779      TCGA-44-7659      TCGA-44-7660      TCGA-44-7661 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-7662      TCGA-44-7667      TCGA-44-7669      TCGA-44-7670 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-7671      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4488      TCGA-49-4490 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4501      TCGA-49-4505      TCGA-49-4506 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-4507      TCGA-49-4510      TCGA-49-4512      TCGA-49-4514 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-49-6745 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-49-6761      TCGA-49-6767      TCGA-50-5044      TCGA-50-5045 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-5049      TCGA-50-5051      TCGA-50-5055      TCGA-50-5066 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-5068      TCGA-50-5072      TCGA-50-5931      TCGA-50-5932 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-5933      TCGA-50-5935      TCGA-50-5936      TCGA-50-5939 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-5941      TCGA-50-5942      TCGA-50-5944      TCGA-50-5946 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-6590      TCGA-50-6591      TCGA-50-6592      TCGA-50-6593 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-6594      TCGA-50-6595      TCGA-50-6597      TCGA-50-6673 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-50-7109      TCGA-50-8457      TCGA-50-8459      TCGA-50-8460 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6543 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6642      TCGA-55-6712      TCGA-55-6968      TCGA-55-6969 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6970      TCGA-55-6971      TCGA-55-6972      TCGA-55-6975 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6978      TCGA-55-6979      TCGA-55-6980      TCGA-55-6981 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6982      TCGA-55-6983      TCGA-55-6984      TCGA-55-6985 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-6986      TCGA-55-6987      TCGA-55-7227      TCGA-55-7281 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7284      TCGA-55-7570      TCGA-55-7573 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7576      TCGA-55-7724      TCGA-55-7725 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7726      TCGA-55-7727      TCGA-55-7816      TCGA-55-7903 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7907      TCGA-55-7910      TCGA-55-7911      TCGA-55-7914 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-7994      TCGA-55-7995      TCGA-55-8085      TCGA-55-8087 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8090      TCGA-55-8091      TCGA-55-8092 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8094      TCGA-55-8096      TCGA-55-8097      TCGA-55-8203 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8204      TCGA-55-8205      TCGA-55-8206      TCGA-55-8207 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8505      TCGA-55-8506      TCGA-55-8507      TCGA-55-8508 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8510      TCGA-55-8511      TCGA-55-8512      TCGA-55-8513 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8614      TCGA-55-8615      TCGA-55-8616 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-55-A4DG      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1676      TCGA-64-1677      TCGA-64-1679 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5774      TCGA-64-5775      TCGA-64-5778 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-64-5779      TCGA-64-5781      TCGA-64-5815      TCGA-67-3771 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-67-3772      TCGA-67-3773      TCGA-67-4679      TCGA-67-6215 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-67-6216      TCGA-67-6217      TCGA-69-7760      TCGA-69-7761 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-7763      TCGA-69-7764      TCGA-69-7765      TCGA-69-7973 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7978      TCGA-69-7979      TCGA-69-7980 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-69-8253      TCGA-69-8254      TCGA-69-8255      TCGA-69-A59K 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4658      TCGA-73-4659 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-4677      TCGA-73-7498 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-73-7499      TCGA-78-7143      TCGA-78-7145      TCGA-78-7146 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7147      TCGA-78-7148      TCGA-78-7149      TCGA-78-7150 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7152      TCGA-78-7153      TCGA-78-7154      TCGA-78-7155 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7156      TCGA-78-7158      TCGA-78-7159      TCGA-78-7160 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7161      TCGA-78-7162      TCGA-78-7163      TCGA-78-7166 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7167      TCGA-78-7220      TCGA-78-7535      TCGA-78-7536 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-78-7539      TCGA-78-7540      TCGA-78-7542      TCGA-78-7633 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6562      TCGA-86-6851      TCGA-86-7701 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7713      TCGA-86-7714      TCGA-86-7953 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8054      TCGA-86-8055 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8075 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8358      TCGA-86-8359      TCGA-86-8585 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-8672 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-8673      TCGA-86-8674      TCGA-86-A456      TCGA-86-A4JF 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-86-A4P7      TCGA-86-A4P8      TCGA-91-6828      TCGA-91-6829 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-6830      TCGA-91-6831      TCGA-91-6835      TCGA-91-6836 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-6840      TCGA-91-6847      TCGA-91-6848      TCGA-91-6849 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-7771      TCGA-91-8496      TCGA-91-8497      TCGA-91-8499 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-91-A4BD      TCGA-93-7347      TCGA-93-7348 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JP 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-93-A4JQ      TCGA-95-7039      TCGA-95-7043      TCGA-95-7562 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-7567      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-8039      TCGA-95-8494      TCGA-95-A4VK      TCGA-95-A4VN 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547      TCGA-97-7552 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7937      TCGA-97-7938 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-7941      TCGA-97-8171      TCGA-97-8172      TCGA-97-8174 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-8175      TCGA-97-8176      TCGA-97-8177      TCGA-97-8179 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-8552      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M6 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025      TCGA-99-8028 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-99-8032      TCGA-99-8033      TCGA-J2-8192      TCGA-J2-8194 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-J2-A4AD      TCGA-J2-A4AE      TCGA-J2-A4AG      TCGA-L4-A4E5 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5      TCGA-MP-A4SW      TCGA-MP-A4SY 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T9 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TD      TCGA-MP-A4TE 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A5C7 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-NJ-A4YF      TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-NJ-A4YP 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-NJ-A4YQ      TCGA-NJ-A55A      TCGA-NJ-A55O      TCGA-NJ-A55R 
"CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" "CRTC3 WILD-TYPE" 
     TCGA-O1-A52J 
"CRTC3 WILD-TYPE" 
D335V15, binary
                 cls
clus                0   1
  CRTC3 MUTATED     0   1
  CRTC3 WILD-TYPE   6 348
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC3 MUTATED      0    1
  CRTC3 WILD-TYPE    6  348
                        clus
vv                       CRTC3 MUTATED CRTC3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             1             348
[1] 2 2
[1] FALSE

Clustering(336) Variable = COL5A3 MUTATION ANALYSIS
D336V1, survival
                  sevent
clus2                0   1
  COL5A3 MUTATED    16   4
  COL5A3 WILD-TYPE 299 137
  COL5A3 MUTATED COL5A3 WILD-TYPE 
              20              436 
  COL5A3 MUTATED COL5A3 WILD-TYPE 
               4              137 
$`COL5A3 MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4420 TCGA-38-4631 TCGA-50-6590 TCGA-53-A4EZ 
       50.07        19.96        29.98        11.64        42.35         9.21 
TCGA-55-1595 TCGA-55-7725 TCGA-55-7994 TCGA-55-8301 TCGA-55-8614 TCGA-55-A4DG 
       48.62         1.28        19.82         1.45        17.62        19.99 
TCGA-62-A46O TCGA-69-7979 TCGA-78-7158 TCGA-86-7955 TCGA-95-7039 TCGA-95-7948 
       47.80         2.93         5.88        16.70         1.12        15.65 
TCGA-97-7546 TCGA-MN-A4N1 
       31.69        27.19 

$`COL5A3 WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
        3.98        14.01        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        23.05         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
        1.08         1.51         2.17        22.16        15.42         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80         6.64         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 
       20.58        19.59         0.92        15.81        20.19         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        6.12        23.61         1.08        19.00        17.29         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.68        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        18.18        19.89        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 
       16.44        19.00        14.30         3.81         0.20        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  COL5A3 MUTATED COL5A3 WILD-TYPE 
            1.12             0.00 
  COL5A3 MUTATED COL5A3 WILD-TYPE 
           50.07           223.96 
  COL5A3 MUTATED COL5A3 WILD-TYPE 
           18.72            18.03 
[1] "1.1 - 50.1 (18.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.4"
D336V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  COL5A3 MUTATED         0        4       11         2         2          0
  COL5A3 WILD-TYPE       4      119      122        44        65         70
                  vv
clus               STAGE IIIB STAGE IV
  COL5A3 MUTATED            1        0
  COL5A3 WILD-TYPE         10       25
D336V3, multiclass
            clus
vv           COL5A3 MUTATED COL5A3 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB               11              122
  STAGE IIA               2               44
  STAGE IIB               2               65
  STAGE IIIA              0               70
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL5A3 MUTATED     4  13   2   1
  COL5A3 WILD-TYPE 151 248  41  17
D336V4, multiclass
    clus
vv   COL5A3 MUTATED COL5A3 WILD-TYPE
  T1              4              151
  T2             13              248
  T3              2               41
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  COL5A3 MUTATED    17   2     1
  COL5A3 WILD-TYPE 290  87    71
D336V5, multiclass
       clus
vv      COL5A3 MUTATED COL5A3 WILD-TYPE
  N0                17              290
  N1                 2               87
  N2+N3              1               71
[1] 3 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
  COL5A3 MUTATED    11   0
  COL5A3 WILD-TYPE 316  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A3 MUTATED     11    0
  COL5A3 WILD-TYPE  316   23
   clus
vv  COL5A3 MUTATED COL5A3 WILD-TYPE
  0             11              316
  1              0               23
[1] 2 2
[1] FALSE
D336V7, binary
                  cls
clus                 0   1
  COL5A3 MUTATED    10  10
  COL5A3 WILD-TYPE 249 211
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A3 MUTATED     10   10
  COL5A3 WILD-TYPE  249  211
        clus
vv       COL5A3 MUTATED COL5A3 WILD-TYPE
  FEMALE             10              249
  MALE               10              211
[1] 2 2
[1] FALSE
D336V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  COL5A3 MUTATED                            3                                 5
  COL5A3 WILD-TYPE                         15                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  COL5A3 MUTATED                                                   11
  COL5A3 WILD-TYPE                                                283
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  COL5A3 MUTATED                                            0
  COL5A3 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  COL5A3 MUTATED                                               0
  COL5A3 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  COL5A3 MUTATED                                1
  COL5A3 WILD-TYPE                              1
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  COL5A3 MUTATED                                    0
  COL5A3 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  COL5A3 MUTATED                              0                             0
  COL5A3 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  COL5A3 MUTATED                                               0
  COL5A3 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  COL5A3 MUTATED                              0
  COL5A3 WILD-TYPE                            9
D336V9, multiclass
                                                    clus
vv                                                   COL5A3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   COL5A3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V10, binary
                  cls
clus                 0   1
  COL5A3 MUTATED     0  20
  COL5A3 WILD-TYPE  20 440
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A3 MUTATED      0   20
  COL5A3 WILD-TYPE   20  440
     clus
vv    COL5A3 MUTATED COL5A3 WILD-TYPE
  NO               0               20
  YES             20              440
[1] 2 2
[1] FALSE
D336V11, continuous
D336V12, continuous
                  vv
clus                R0  R1  R2  RX
  COL5A3 MUTATED    13   1   0   2
  COL5A3 WILD-TYPE 297  10   4  23
D336V13, multiclass
    clus
vv   COL5A3 MUTATED COL5A3 WILD-TYPE
  R0             13              297
  R1              1               10
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL5A3 MUTATED                                  0     1
  COL5A3 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL5A3 MUTATED                           1    15
  COL5A3 WILD-TYPE                        28   362
D336V14, multiclass
                                  clus
vv                                 COL5A3 MUTATED COL5A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        15              362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V15, binary
                  cls
clus                 0   1
  COL5A3 MUTATED     1  15
  COL5A3 WILD-TYPE   5 334
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A3 MUTATED      1   15
  COL5A3 WILD-TYPE    5  334
                        clus
vv                       COL5A3 MUTATED COL5A3 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             15              334
[1] 2 2
[1] FALSE

Clustering(337) Variable = SF1 MUTATION ANALYSIS
D337V1, survival
               sevent
clus2             0   1
  SF1 MUTATED     6   5
  SF1 WILD-TYPE 309 136
  SF1 MUTATED SF1 WILD-TYPE 
           11           445 
  SF1 MUTATED SF1 WILD-TYPE 
            5           136 
$`SF1 MUTATED`
TCGA-05-4422 TCGA-38-4625 TCGA-38-4631 TCGA-38-4632 TCGA-44-7669 TCGA-50-5930 
       12.00        97.74        11.64        44.61        18.87         9.27 
TCGA-55-7227 TCGA-55-7995 TCGA-62-A470 TCGA-86-8073 TCGA-99-8032 
        1.74         0.16        39.25        24.33         1.45 

$`SF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 
       20.05         2.99        14.96         9.01        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       49.05        28.41        35.28        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03         7.17        36.07        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        8.22        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       70.26         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        72.30        13.61        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85        36.76         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SF1 MUTATED SF1 WILD-TYPE 
         0.16          0.00 
  SF1 MUTATED SF1 WILD-TYPE 
        97.74        223.96 
  SF1 MUTATED SF1 WILD-TYPE 
        12.00         18.08 
[1] "0.2 - 97.7 (12.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D337V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SF1 MUTATED         0        2        5         1         1          2
  SF1 WILD-TYPE       4      121      128        45        66         68
               vv
clus            STAGE IIIB STAGE IV
  SF1 MUTATED            0        1
  SF1 WILD-TYPE         11       24
D337V3, multiclass
            clus
vv           SF1 MUTATED SF1 WILD-TYPE
  STAGE I              0             4
  STAGE IA             2           121
  STAGE IB             5           128
  STAGE IIA            1            45
  STAGE IIB            1            66
  STAGE IIIA           2            68
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SF1 MUTATED     3   8   1   0
  SF1 WILD-TYPE 152 253  42  18
D337V4, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  T1           3           152
  T2           8           253
  T3           1            42
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  SF1 MUTATED     7   4     1
  SF1 WILD-TYPE 300  85    71
D337V5, multiclass
       clus
vv      SF1 MUTATED SF1 WILD-TYPE
  N0              7           300
  N1              4            85
  N2+N3           1            71
[1] 3 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
  SF1 MUTATED     9   1
  SF1 WILD-TYPE 318  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      9    1
  SF1 WILD-TYPE  318   22
   clus
vv  SF1 MUTATED SF1 WILD-TYPE
  0           9           318
  1           1            22
[1] 2 2
[1] FALSE
D337V7, binary
               cls
clus              0   1
  SF1 MUTATED     3   9
  SF1 WILD-TYPE 256 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      3    9
  SF1 WILD-TYPE  256  212
        clus
vv       SF1 MUTATED SF1 WILD-TYPE
  FEMALE           3           256
  MALE             9           212
[1] 2 2
[1] FALSE
D337V8, continuous
[1] "Remove cluster labels:" "SF1 MUTATED"           
clus
  SF1 MUTATED SF1 WILD-TYPE 
            1            83 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8089 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-55-8096    TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-55-8511    TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-55-A490    TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-62-8398    TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-62-A46R    TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681    TCGA-64-5778 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520    TCGA-73-4659 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-86-7713    TCGA-86-7714    TCGA-86-7954    TCGA-86-7955    TCGA-86-8055 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-86-8056    TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-86-8279    TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-86-8669    TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
   TCGA-MN-A4N1    TCGA-MN-A4N4    TCGA-MN-A4N5 
"SF1 WILD-TYPE" "SF1 WILD-TYPE" "SF1 WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SF1 MUTATED                            1                                 2
  SF1 WILD-TYPE                         17                               100
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SF1 MUTATED                                                    8
  SF1 WILD-TYPE                                                286
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SF1 MUTATED                                            0
  SF1 WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SF1 MUTATED                                               1
  SF1 WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  SF1 MUTATED                                0
  SF1 WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  SF1 MUTATED                                    0                            0
  SF1 WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  SF1 MUTATED                               0
  SF1 WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SF1 MUTATED                                               0
  SF1 WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  SF1 MUTATED                              0
  SF1 WILD-TYPE                            9
D337V9, multiclass
                                                    clus
vv                                                   SF1 MUTATED SF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            2           100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           8           286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V10, binary
               cls
clus              0   1
  SF1 MUTATED     1  11
  SF1 WILD-TYPE  19 449
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      1   11
  SF1 WILD-TYPE   19  449
     clus
vv    SF1 MUTATED SF1 WILD-TYPE
  NO            1            19
  YES          11           449
[1] 2 2
[1] FALSE
D337V11, continuous
D337V12, continuous
               vv
clus             R0  R1  R2  RX
  SF1 MUTATED     9   0   0   0
  SF1 WILD-TYPE 301  11   4  25
D337V13, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  R0           9           301
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SF1 MUTATED                                  0     0
  SF1 WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SF1 MUTATED                           2     8
  SF1 WILD-TYPE                        27   369
D337V14, multiclass
                                  clus
vv                                 SF1 MUTATED SF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  2            27
  WHITE                                      8           369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V15, binary
               cls
clus              0   1
  SF1 MUTATED     0  10
  SF1 WILD-TYPE   6 339
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      0   10
  SF1 WILD-TYPE    6  339
                        clus
vv                       SF1 MUTATED SF1 WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          10           339
[1] 2 2
[1] FALSE

Clustering(338) Variable = ZCCHC11 MUTATION ANALYSIS
D338V1, survival
                   sevent
clus2                 0   1
  ZCCHC11 MUTATED     6   6
  ZCCHC11 WILD-TYPE 309 135
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               12               444 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                6               135 
$`ZCCHC11 MUTATED`
TCGA-05-4395 TCGA-44-8119 TCGA-50-5933 TCGA-53-7624 TCGA-64-1679 TCGA-78-7145 
        0.00         3.25        78.67        34.29        55.43        27.16 
TCGA-86-7713 TCGA-86-8359 TCGA-95-7944 TCGA-95-A4VN TCGA-97-A4M3 TCGA-MP-A4T7 
       13.87        14.60        12.39        18.18        17.75         5.49 

$`ZCCHC11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        21.47         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 
       17.29         1.12         1.22         2.86        18.67        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29         2.76        21.40        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       19.76        20.52        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
             0.00              0.07 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
            78.67            223.96 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
           16.175            18.100 
[1] "0.0 - 78.7 (16.2)"  "0.1 - 224.0 (18.1)"
[1] "hr=" "1.6"
D338V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZCCHC11 MUTATED         0        2        0         2         1          2
  ZCCHC11 WILD-TYPE       4      121      133        44        66         68
                   vv
clus                STAGE IIIB STAGE IV
  ZCCHC11 MUTATED            2        3
  ZCCHC11 WILD-TYPE          9       22
D338V3, multiclass
            clus
vv           ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 0               133
  STAGE IIA                2                44
  STAGE IIB                1                66
  STAGE IIIA               2                68
  STAGE IIIB               2                 9
  STAGE IV                 3                22
[1] 8 2
[1] TRUE
[1] "dimension of 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     3   4   2   3
  ZCCHC11 WILD-TYPE 152 257  41  15
D338V4, multiclass
    clus
vv   ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  T1               3               152
  T2               4               257
  T3               2                41
  T4               3                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"
                   vv
clus                 N0  N1 N2+N3
  ZCCHC11 MUTATED     6   2     4
  ZCCHC11 WILD-TYPE 301  87    68
D338V5, multiclass
       clus
vv      ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  N0                  6               301
  N1                  2                87
  N2+N3               4                68
[1] 3 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
  ZCCHC11 MUTATED     9   3
  ZCCHC11 WILD-TYPE 318  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      9    3
  ZCCHC11 WILD-TYPE  318   20
   clus
vv  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  0               9               318
  1               3                20
[1] 2 2
[1] FALSE
D338V7, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED     6   6
  ZCCHC11 WILD-TYPE 253 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      6    6
  ZCCHC11 WILD-TYPE  253  215
        clus
vv       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  FEMALE               6               253
  MALE                 6               215
[1] 2 2
[1] FALSE
D338V8, continuous
[1] "Remove cluster labels:" "ZCCHC11 MUTATED"       
clus
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-86-8668        TCGA-86-8669        TCGA-86-8671        TCGA-86-A4JF 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ZCCHC11 MUTATED                            0
  ZCCHC11 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZCCHC11 MUTATED                                   2
  ZCCHC11 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC11 MUTATED                                                    9
  ZCCHC11 WILD-TYPE                                                285
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZCCHC11 MUTATED                                            0
  ZCCHC11 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZCCHC11 MUTATED                                               0
  ZCCHC11 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ZCCHC11 MUTATED                                0
  ZCCHC11 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ZCCHC11 MUTATED                                    0
  ZCCHC11 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZCCHC11 MUTATED                              0                             0
  ZCCHC11 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZCCHC11 MUTATED                                               1
  ZCCHC11 WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ZCCHC11 MUTATED                              0
  ZCCHC11 WILD-TYPE                            9
D338V9, multiclass
                                                    clus
vv                                                   ZCCHC11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ZCCHC11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V10, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED     1  11
  ZCCHC11 WILD-TYPE  19 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      1   11
  ZCCHC11 WILD-TYPE   19  449
     clus
vv    ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  NO                1                19
  YES              11               449
[1] 2 2
[1] FALSE
D338V11, continuous
D338V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ZCCHC11 MUTATED     8   1   0   0
  ZCCHC11 WILD-TYPE 302  10   4  25
D338V13, multiclass
    clus
vv   ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  R0               8               302
  R1               1                10
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZCCHC11 MUTATED                                  0     0
  ZCCHC11 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZCCHC11 MUTATED                           0    10
  ZCCHC11 WILD-TYPE                        29   367
D338V14, multiclass
                                  clus
vv                                 ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                         10               367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V15, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED     1   8
  ZCCHC11 WILD-TYPE   5 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      1    8
  ZCCHC11 WILD-TYPE    5  341
                        clus
vv                       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               8               341
[1] 2 2
[1] FALSE

Clustering(339) Variable = AIFM1 MUTATION ANALYSIS
D339V1, survival
                 sevent
clus2               0   1
  AIFM1 MUTATED     9   3
  AIFM1 WILD-TYPE 306 138
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             12             444 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
              3             138 
$`AIFM1 MUTATED`
TCGA-38-4631 TCGA-44-6774 TCGA-50-6594 TCGA-55-8506 TCGA-55-A48X TCGA-55-A494 
       11.64        21.63        12.16         0.36        22.65        15.81 
TCGA-69-7974 TCGA-86-A456 TCGA-86-A4P7 TCGA-95-7043 TCGA-97-7938 TCGA-97-A4M3 
        6.05        13.32        13.64         1.22         0.59        17.75 

$`AIFM1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        16.93        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58        19.59         0.92        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
       30.84        27.58         0.62        14.96        13.32        17.62 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
       64.60        63.52        43.79        25.48         5.95         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       20.52        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  AIFM1 MUTATED AIFM1 WILD-TYPE 
           0.36            0.00 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
          22.65          223.96 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
          12.74           18.64 
[1] "0.4 - 22.6 (12.7)"  "0.0 - 224.0 (18.6)"
[1] "hr=" "2.1"
D339V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AIFM1 MUTATED         0        4        4         1         1          3
  AIFM1 WILD-TYPE       4      119      129        45        66         67
                 vv
clus              STAGE IIIB STAGE IV
  AIFM1 MUTATED            0        0
  AIFM1 WILD-TYPE         11       25
D339V3, multiclass
            clus
vv           AIFM1 MUTATED AIFM1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               4             129
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AIFM1 MUTATED     6   5   2   0
  AIFM1 WILD-TYPE 149 256  41  18
D339V4, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  T1             6             149
  T2             5             256
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  AIFM1 MUTATED     9   1     3
  AIFM1 WILD-TYPE 298  88    69
D339V5, multiclass
       clus
vv      AIFM1 MUTATED AIFM1 WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             3              69
[1] 3 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
  AIFM1 MUTATED     8   0
  AIFM1 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      8    0
  AIFM1 WILD-TYPE  319   23
   clus
vv  AIFM1 MUTATED AIFM1 WILD-TYPE
  0             8             319
  1             0              23
[1] 2 2
[1] FALSE
D339V7, binary
                 cls
clus                0   1
  AIFM1 MUTATED    13   0
  AIFM1 WILD-TYPE 246 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED     13    0
  AIFM1 WILD-TYPE  246  221
        clus
vv       AIFM1 MUTATED AIFM1 WILD-TYPE
  FEMALE            13             246
  MALE               0             221
[1] 2 2
[1] FALSE
D339V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AIFM1 MUTATED                            0                                 3
  AIFM1 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AIFM1 MUTATED                                                    8
  AIFM1 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AIFM1 MUTATED                                            0
  AIFM1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AIFM1 MUTATED                                               1
  AIFM1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  AIFM1 MUTATED                                0
  AIFM1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  AIFM1 MUTATED                                    0
  AIFM1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  AIFM1 MUTATED                              0                             1
  AIFM1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AIFM1 MUTATED                                               0
  AIFM1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  AIFM1 MUTATED                              0
  AIFM1 WILD-TYPE                            9
D339V9, multiclass
                                                    clus
vv                                                   AIFM1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   AIFM1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V10, binary
                 cls
clus                0   1
  AIFM1 MUTATED     2  11
  AIFM1 WILD-TYPE  18 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      2   11
  AIFM1 WILD-TYPE   18  449
     clus
vv    AIFM1 MUTATED AIFM1 WILD-TYPE
  NO              2              18
  YES            11             449
[1] 2 2
[1] FALSE
D339V11, continuous
D339V12, continuous
                 vv
clus               R0  R1  R2  RX
  AIFM1 MUTATED     8   0   0   0
  AIFM1 WILD-TYPE 302  11   4  25
D339V13, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AIFM1 MUTATED                                  0     1
  AIFM1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AIFM1 MUTATED                           1    10
  AIFM1 WILD-TYPE                        28   367
D339V14, multiclass
                                  clus
vv                                 AIFM1 MUTATED AIFM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V15, binary
                 cls
clus                0   1
  AIFM1 MUTATED     0  12
  AIFM1 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      0   12
  AIFM1 WILD-TYPE    6  337
                        clus
vv                       AIFM1 MUTATED AIFM1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(340) Variable = DCAF8 MUTATION ANALYSIS
D340V1, survival
                 sevent
clus2               0   1
  DCAF8 MUTATED     6   6
  DCAF8 WILD-TYPE 309 135
  DCAF8 MUTATED DCAF8 WILD-TYPE 
             12             444 
  DCAF8 MUTATED DCAF8 WILD-TYPE 
              6             135 
$`DCAF8 MUTATED`
TCGA-05-4396 TCGA-05-4424 TCGA-05-4427 TCGA-38-4625 TCGA-44-8117 TCGA-49-4487 
        9.96        30.02        26.01        97.74        12.66        28.11 
TCGA-55-8299 TCGA-62-A46O TCGA-67-3771 TCGA-78-7542 TCGA-78-8662 TCGA-NJ-A4YQ 
       15.42        47.80        20.05        10.55       110.50        29.13 

$`DCAF8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        5.98         8.68       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        13.15        24.36        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        10.75        39.35        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  DCAF8 MUTATED DCAF8 WILD-TYPE 
           9.96            0.00 
  DCAF8 MUTATED DCAF8 WILD-TYPE 
         110.50          223.96 
  DCAF8 MUTATED DCAF8 WILD-TYPE 
         27.060          17.835 
[1] "10.0 - 110.5 (27.1)" "0.0 - 224.0 (17.8)" 
[1] "hr=" "1"  
D340V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DCAF8 MUTATED         0        4        5         0         2          0
  DCAF8 WILD-TYPE       4      119      128        46        65         70
                 vv
clus              STAGE IIIB STAGE IV
  DCAF8 MUTATED            1        0
  DCAF8 WILD-TYPE         10       25
D340V3, multiclass
            clus
vv           DCAF8 MUTATED DCAF8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               5             128
  STAGE IIA              0              46
  STAGE IIB              2              65
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCAF8 MUTATED     4   6   1   1
  DCAF8 WILD-TYPE 151 255  42  17
D340V4, multiclass
    clus
vv   DCAF8 MUTATED DCAF8 WILD-TYPE
  T1             4             151
  T2             6             255
  T3             1              42
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  DCAF8 MUTATED    10   2     0
  DCAF8 WILD-TYPE 297  87    72
D340V5, multiclass
       clus
vv      DCAF8 MUTATED DCAF8 WILD-TYPE
  N0               10             297
  N1                2              87
  N2+N3             0              72
[1] 3 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
  DCAF8 MUTATED    11   0
  DCAF8 WILD-TYPE 316  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF8 MUTATED     11    0
  DCAF8 WILD-TYPE  316   23
   clus
vv  DCAF8 MUTATED DCAF8 WILD-TYPE
  0            11             316
  1             0              23
[1] 2 2
[1] FALSE
D340V7, binary
                 cls
clus                0   1
  DCAF8 MUTATED     9   3
  DCAF8 WILD-TYPE 250 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF8 MUTATED      9    3
  DCAF8 WILD-TYPE  250  218
        clus
vv       DCAF8 MUTATED DCAF8 WILD-TYPE
  FEMALE             9             250
  MALE               3             218
[1] 2 2
[1] FALSE
D340V8, continuous
[1] "Remove cluster labels:" "DCAF8 MUTATED"         
clus
  DCAF8 MUTATED DCAF8 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" "DCAF8 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DCAF8 MUTATED                            0                                 3
  DCAF8 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DCAF8 MUTATED                                                    9
  DCAF8 WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DCAF8 MUTATED                                            0
  DCAF8 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DCAF8 MUTATED                                               0
  DCAF8 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  DCAF8 MUTATED                                0
  DCAF8 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  DCAF8 MUTATED                                    0
  DCAF8 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DCAF8 MUTATED                              0                             0
  DCAF8 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DCAF8 MUTATED                                               0
  DCAF8 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  DCAF8 MUTATED                              0
  DCAF8 WILD-TYPE                            9
D340V9, multiclass
                                                    clus
vv                                                   DCAF8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   DCAF8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V10, binary
                 cls
clus                0   1
  DCAF8 MUTATED     0  12
  DCAF8 WILD-TYPE  20 448
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF8 MUTATED      0   12
  DCAF8 WILD-TYPE   20  448
     clus
vv    DCAF8 MUTATED DCAF8 WILD-TYPE
  NO              0              20
  YES            12             448
[1] 2 2
[1] FALSE
D340V11, continuous
D340V12, continuous
                 vv
clus               R0  R1  R2  RX
  DCAF8 MUTATED     9   1   0   1
  DCAF8 WILD-TYPE 301  10   4  24
D340V13, multiclass
    clus
vv   DCAF8 MUTATED DCAF8 WILD-TYPE
  R0             9             301
  R1             1              10
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCAF8 MUTATED                                  0     0
  DCAF8 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCAF8 MUTATED                           1     7
  DCAF8 WILD-TYPE                        28   370
D340V14, multiclass
                                  clus
vv                                 DCAF8 MUTATED DCAF8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V15, binary
                 cls
clus                0   1
  DCAF8 MUTATED     0   7
  DCAF8 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF8 MUTATED      0    7
  DCAF8 WILD-TYPE    6  342
                        clus
vv                       DCAF8 MUTATED DCAF8 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(341) Variable = PPP2R2A MUTATION ANALYSIS
D341V1, survival
                   sevent
clus2                 0   1
  PPP2R2A MUTATED     5   1
  PPP2R2A WILD-TYPE 310 140
  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
                6               450 
  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
                1               140 
$`PPP2R2A MUTATED`
TCGA-05-4398 TCGA-44-A47A TCGA-55-8302 TCGA-69-7974 TCGA-86-8279 TCGA-MP-A4SV 
       47.05        15.32         0.76         6.05        15.85        86.14 

$`PPP2R2A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.98         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         7.56         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       15.75        16.08        15.65        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19        38.63         2.76        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
             0.76              0.00 
  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
            86.14            223.96 
  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
           15.585            18.100 
[1] "0.8 - 86.1 (15.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.6"
D341V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PPP2R2A MUTATED         0        0        3         1         0          1
  PPP2R2A WILD-TYPE       4      123      130        45        67         69
                   vv
clus                STAGE IIIB STAGE IV
  PPP2R2A MUTATED            1        0
  PPP2R2A WILD-TYPE         10       25
D341V3, multiclass
            clus
vv           PPP2R2A MUTATED PPP2R2A WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0               123
  STAGE IB                 3               130
  STAGE IIA                1                45
  STAGE IIB                0                67
  STAGE IIIA               1                69
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP2R2A MUTATED     0   5   0   1
  PPP2R2A WILD-TYPE 155 256  43  17
D341V4, multiclass
    clus
vv   PPP2R2A MUTATED PPP2R2A WILD-TYPE
  T1               0               155
  T2               5               256
  T3               0                43
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  PPP2R2A MUTATED     3   1     2
  PPP2R2A WILD-TYPE 304  88    70
D341V5, multiclass
       clus
vv      PPP2R2A MUTATED PPP2R2A WILD-TYPE
  N0                  3               304
  N1                  1                88
  N2+N3               2                70
[1] 3 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
  PPP2R2A MUTATED     3   0
  PPP2R2A WILD-TYPE 324  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2A MUTATED      3    0
  PPP2R2A WILD-TYPE  324   23
   clus
vv  PPP2R2A MUTATED PPP2R2A WILD-TYPE
  0               3               324
  1               0                23
[1] 2 2
[1] FALSE
D341V7, binary
                   cls
clus                  0   1
  PPP2R2A MUTATED     3   3
  PPP2R2A WILD-TYPE 256 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2A MUTATED      3    3
  PPP2R2A WILD-TYPE  256  218
        clus
vv       PPP2R2A MUTATED PPP2R2A WILD-TYPE
  FEMALE               3               256
  MALE                 3               218
[1] 2 2
[1] FALSE
D341V8, continuous
[1] "Remove cluster labels:" "PPP2R2A MUTATED"       
clus
  PPP2R2A MUTATED PPP2R2A WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-64-5778        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8281        TCGA-86-8358        TCGA-86-8359 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-86-8668        TCGA-86-8669        TCGA-86-8671        TCGA-86-A4JF 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"PPP2R2A WILD-TYPE" "PPP2R2A WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PPP2R2A MUTATED                            0
  PPP2R2A WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PPP2R2A MUTATED                                   2
  PPP2R2A WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PPP2R2A MUTATED                                                    4
  PPP2R2A WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PPP2R2A MUTATED                                            0
  PPP2R2A WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PPP2R2A MUTATED                                               0
  PPP2R2A WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  PPP2R2A MUTATED                                0
  PPP2R2A WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  PPP2R2A MUTATED                                    0
  PPP2R2A WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PPP2R2A MUTATED                              0                             0
  PPP2R2A WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PPP2R2A MUTATED                                               0
  PPP2R2A WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  PPP2R2A MUTATED                              0
  PPP2R2A WILD-TYPE                            9
D341V9, multiclass
                                                    clus
vv                                                   PPP2R2A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   PPP2R2A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V10, binary
                   cls
clus                  0   1
  PPP2R2A MUTATED     1   5
  PPP2R2A WILD-TYPE  19 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2A MUTATED      1    5
  PPP2R2A WILD-TYPE   19  455
     clus
vv    PPP2R2A MUTATED PPP2R2A WILD-TYPE
  NO                1                19
  YES               5               455
[1] 2 2
[1] FALSE
D341V11, continuous
D341V12, continuous
                   vv
clus                 R0  R1  R2  RX
  PPP2R2A MUTATED     5   0   0   0
  PPP2R2A WILD-TYPE 305  11   4  25
D341V13, multiclass
    clus
vv   PPP2R2A MUTATED PPP2R2A WILD-TYPE
  R0               5               305
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R2A MUTATED                                  0     0
  PPP2R2A WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R2A MUTATED                           0     4
  PPP2R2A WILD-TYPE                        29   373
D341V14, multiclass
                                  clus
vv                                 PPP2R2A MUTATED PPP2R2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          4               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V15, binary
                   cls
clus                  0   1
  PPP2R2A MUTATED     0   3
  PPP2R2A WILD-TYPE   6 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2A MUTATED      0    3
  PPP2R2A WILD-TYPE    6  346
                        clus
vv                       PPP2R2A MUTATED PPP2R2A WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               346
[1] 2 2
[1] FALSE

Clustering(342) Variable = IRF6 MUTATION ANALYSIS
D342V1, survival
                sevent
clus2              0   1
  IRF6 MUTATED     7   2
  IRF6 WILD-TYPE 308 139
  IRF6 MUTATED IRF6 WILD-TYPE 
             9            447 
  IRF6 MUTATED IRF6 WILD-TYPE 
             2            139 
$`IRF6 MUTATED`
TCGA-05-4427 TCGA-05-4432 TCGA-38-4631 TCGA-44-8117 TCGA-55-7911 TCGA-55-7995 
       26.01        25.02        11.64        12.66        17.65         0.16 
TCGA-55-A490 TCGA-MP-A4TA TCGA-NJ-A55O 
        1.58        31.23         0.43 

$`IRF6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       30.02        21.99        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.00        17.59        23.64         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
       18.64         0.53         6.48         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
       86.04        58.85         5.49         5.29        41.59         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J 
        0.26        19.82        59.11 

  IRF6 MUTATED IRF6 WILD-TYPE 
          0.16           0.00 
  IRF6 MUTATED IRF6 WILD-TYPE 
         31.23         223.96 
  IRF6 MUTATED IRF6 WILD-TYPE 
         12.66          18.12 
[1] "0.2 - 31.2 (12.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D342V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  IRF6 MUTATED         0        3        2         2         2          0
  IRF6 WILD-TYPE       4      120      131        44        65         70
                vv
clus             STAGE IIIB STAGE IV
  IRF6 MUTATED            0        0
  IRF6 WILD-TYPE         11       25
D342V3, multiclass
            clus
vv           IRF6 MUTATED IRF6 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              2            131
  STAGE IIA             2             44
  STAGE IIB             2             65
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRF6 MUTATED     4   5   0   0
  IRF6 WILD-TYPE 151 256  43  18
D342V4, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  T1            4            151
  T2            5            256
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  IRF6 MUTATED     6   3     0
  IRF6 WILD-TYPE 301  86    72
D342V5, multiclass
       clus
vv      IRF6 MUTATED IRF6 WILD-TYPE
  N0               6            301
  N1               3             86
  N2+N3            0             72
[1] 3 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
  IRF6 MUTATED     7   0
  IRF6 WILD-TYPE 320  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      7    0
  IRF6 WILD-TYPE  320   23
   clus
vv  IRF6 MUTATED IRF6 WILD-TYPE
  0            7            320
  1            0             23
[1] 2 2
[1] FALSE
D342V7, binary
                cls
clus               0   1
  IRF6 MUTATED     7   2
  IRF6 WILD-TYPE 252 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      7    2
  IRF6 WILD-TYPE  252  219
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  FEMALE            7            252
  MALE              2            219
[1] 2 2
[1] FALSE
D342V8, continuous
[1] "Remove cluster labels:" "IRF6 MUTATED"          
clus
  IRF6 MUTATED IRF6 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  IRF6 MUTATED                            0                                 2
  IRF6 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IRF6 MUTATED                                                    6
  IRF6 WILD-TYPE                                                288
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  IRF6 MUTATED                                            0
  IRF6 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  IRF6 MUTATED                                               0
  IRF6 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  IRF6 MUTATED                                0
  IRF6 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  IRF6 MUTATED                                    0
  IRF6 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  IRF6 MUTATED                              0                             0
  IRF6 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  IRF6 MUTATED                                               0
  IRF6 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  IRF6 MUTATED                              1
  IRF6 WILD-TYPE                            8
D342V9, multiclass
                                                    clus
vv                                                   IRF6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   IRF6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V10, binary
                cls
clus               0   1
  IRF6 MUTATED     0   9
  IRF6 WILD-TYPE  20 451
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      0    9
  IRF6 WILD-TYPE   20  451
     clus
vv    IRF6 MUTATED IRF6 WILD-TYPE
  NO             0             20
  YES            9            451
[1] 2 2
[1] FALSE
D342V11, continuous
D342V12, continuous
                vv
clus              R0  R1  R2  RX
  IRF6 MUTATED     7   0   0   0
  IRF6 WILD-TYPE 303  11   4  25
D342V13, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRF6 MUTATED                                  0     0
  IRF6 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRF6 MUTATED                           0     7
  IRF6 WILD-TYPE                        29   370
D342V14, multiclass
                                  clus
vv                                 IRF6 MUTATED IRF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V15, binary
                cls
clus               0   1
  IRF6 MUTATED     0   7
  IRF6 WILD-TYPE   6 342
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      0    7
  IRF6 WILD-TYPE    6  342
                        clus
vv                       IRF6 MUTATED IRF6 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            7            342
[1] 2 2
[1] FALSE

Clustering(343) Variable = SIRPA MUTATION ANALYSIS
D343V1, survival
                 sevent
clus2               0   1
  SIRPA MUTATED     7   2
  SIRPA WILD-TYPE 308 139
  SIRPA MUTATED SIRPA WILD-TYPE 
              9             447 
  SIRPA MUTATED SIRPA WILD-TYPE 
              2             139 
$`SIRPA MUTATED`
TCGA-05-4405 TCGA-05-4430 TCGA-44-6774 TCGA-69-7765 TCGA-78-7155 TCGA-95-7562 
       20.05        25.02        21.63         5.42        38.50         2.86 
TCGA-95-A4VP TCGA-99-8028 TCGA-NJ-A4YP 
       19.89        36.76         1.64 

$`SIRPA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        18.18        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 
       20.84        18.67        20.68        24.56        34.85         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SIRPA MUTATED SIRPA WILD-TYPE 
           1.64            0.00 
  SIRPA MUTATED SIRPA WILD-TYPE 
          38.50          223.96 
  SIRPA MUTATED SIRPA WILD-TYPE 
          20.05           17.92 
[1] "1.6 - 38.5 (20.1)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.1"
D343V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SIRPA MUTATED         0        1        5         1         0          2
  SIRPA WILD-TYPE       4      122      128        45        67         68
                 vv
clus              STAGE IIIB STAGE IV
  SIRPA MUTATED            0        1
  SIRPA WILD-TYPE         11       24
D343V3, multiclass
            clus
vv           SIRPA MUTATED SIRPA WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               5             128
  STAGE IIA              1              45
  STAGE IIB              0              67
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SIRPA MUTATED     2   7   0   1
  SIRPA WILD-TYPE 153 254  43  17
D343V4, multiclass
    clus
vv   SIRPA MUTATED SIRPA WILD-TYPE
  T1             2             153
  T2             7             254
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  SIRPA MUTATED     7   1     2
  SIRPA WILD-TYPE 300  88    70
D343V5, multiclass
       clus
vv      SIRPA MUTATED SIRPA WILD-TYPE
  N0                7             300
  N1                1              88
  N2+N3             2              70
[1] 3 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
  SIRPA MUTATED     9   0
  SIRPA WILD-TYPE 318  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      9    0
  SIRPA WILD-TYPE  318   23
   clus
vv  SIRPA MUTATED SIRPA WILD-TYPE
  0             9             318
  1             0              23
[1] 2 2
[1] FALSE
D343V7, binary
                 cls
clus                0   1
  SIRPA MUTATED     5   5
  SIRPA WILD-TYPE 254 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      5    5
  SIRPA WILD-TYPE  254  216
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  FEMALE             5             254
  MALE               5             216
[1] 2 2
[1] FALSE
D343V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SIRPA MUTATED                            1                                 4
  SIRPA WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SIRPA MUTATED                                                    4
  SIRPA WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SIRPA MUTATED                                            0
  SIRPA WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SIRPA MUTATED                                               0
  SIRPA WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SIRPA MUTATED                                0
  SIRPA WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SIRPA MUTATED                                    0
  SIRPA WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SIRPA MUTATED                              0                             1
  SIRPA WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SIRPA MUTATED                                               0
  SIRPA WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SIRPA MUTATED                              0
  SIRPA WILD-TYPE                            9
D343V9, multiclass
                                                    clus
vv                                                   SIRPA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SIRPA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V10, binary
                 cls
clus                0   1
  SIRPA MUTATED     1   9
  SIRPA WILD-TYPE  19 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      1    9
  SIRPA WILD-TYPE   19  451
     clus
vv    SIRPA MUTATED SIRPA WILD-TYPE
  NO              1              19
  YES             9             451
[1] 2 2
[1] FALSE
D343V11, continuous
D343V12, continuous
                 vv
clus               R0  R1  R2  RX
  SIRPA MUTATED     4   0   0   2
  SIRPA WILD-TYPE 306  11   4  23
D343V13, multiclass
    clus
vv   SIRPA MUTATED SIRPA WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIRPA MUTATED                                  0     0
  SIRPA WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SIRPA MUTATED                           3     4
  SIRPA WILD-TYPE                        26   373
D343V14, multiclass
                                  clus
vv                                 SIRPA MUTATED SIRPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              26
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V15, binary
                 cls
clus                0   1
  SIRPA MUTATED     0   5
  SIRPA WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      0    5
  SIRPA WILD-TYPE    6  344
                        clus
vv                       SIRPA MUTATED SIRPA WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(344) Variable = ANGPT4 MUTATION ANALYSIS
D344V1, survival
                  sevent
clus2                0   1
  ANGPT4 MUTATED     7   3
  ANGPT4 WILD-TYPE 308 138
  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
              10              446 
  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
               3              138 
$`ANGPT4 MUTATED`
TCGA-05-4397 TCGA-44-5644 TCGA-50-6590 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-8507 
       24.03        28.37        42.35        34.29         9.21         0.26 
TCGA-69-7979 TCGA-86-8073 TCGA-95-A4VN TCGA-97-A4LX 
        2.93        24.33        18.18        20.19 

$`ANGPT4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        22.55         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 
        7.59        27.25        30.54        13.94        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.36         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP 
       15.68        15.65        27.29         2.76        21.40        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
            0.26             0.00 
  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
           42.35           223.96 
  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
          22.110           17.835 
[1] "0.3 - 42.4 (22.1)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.2"
D344V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ANGPT4 MUTATED         0        1        6         2         1          0
  ANGPT4 WILD-TYPE       4      122      127        44        66         70
                  vv
clus               STAGE IIIB STAGE IV
  ANGPT4 MUTATED            0        1
  ANGPT4 WILD-TYPE         11       24
D344V3, multiclass
            clus
vv           ANGPT4 MUTATED ANGPT4 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                6              127
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANGPT4 MUTATED     1  10   0   0
  ANGPT4 WILD-TYPE 154 251  43  18
D344V4, multiclass
    clus
vv   ANGPT4 MUTATED ANGPT4 WILD-TYPE
  T1              1              154
  T2             10              251
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ANGPT4 MUTATED     8   3     0
  ANGPT4 WILD-TYPE 299  86    72
D344V5, multiclass
       clus
vv      ANGPT4 MUTATED ANGPT4 WILD-TYPE
  N0                 8              299
  N1                 3               86
  N2+N3              0               72
[1] 3 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
  ANGPT4 MUTATED     6   1
  ANGPT4 WILD-TYPE 321  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANGPT4 MUTATED      6    1
  ANGPT4 WILD-TYPE  321   22
   clus
vv  ANGPT4 MUTATED ANGPT4 WILD-TYPE
  0              6              321
  1              1               22
[1] 2 2
[1] FALSE
D344V7, binary
                  cls
clus                 0   1
  ANGPT4 MUTATED     5   6
  ANGPT4 WILD-TYPE 254 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANGPT4 MUTATED      5    6
  ANGPT4 WILD-TYPE  254  215
        clus
vv       ANGPT4 MUTATED ANGPT4 WILD-TYPE
  FEMALE              5              254
  MALE                6              215
[1] 2 2
[1] FALSE
D344V8, continuous
[1] "Remove cluster labels:" "ANGPT4 MUTATED"        
clus
  ANGPT4 MUTATED ANGPT4 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-55-7283 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-55-7573       TCGA-55-7725       TCGA-55-7910       TCGA-55-7914 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-55-8089       TCGA-55-8096       TCGA-55-8205       TCGA-55-8208 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8511       TCGA-55-8512       TCGA-55-8619 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5778       TCGA-69-7974 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4676 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"ANGPT4 WILD-TYPE" "ANGPT4 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ANGPT4 MUTATED                            2                                 2
  ANGPT4 WILD-TYPE                         16                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ANGPT4 MUTATED                                                    5
  ANGPT4 WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ANGPT4 MUTATED                                            0
  ANGPT4 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ANGPT4 MUTATED                                               1
  ANGPT4 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ANGPT4 MUTATED                                0
  ANGPT4 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ANGPT4 MUTATED                                    0
  ANGPT4 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ANGPT4 MUTATED                              0                             0
  ANGPT4 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ANGPT4 MUTATED                                               1
  ANGPT4 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ANGPT4 MUTATED                              0
  ANGPT4 WILD-TYPE                            9
D344V9, multiclass
                                                    clus
vv                                                   ANGPT4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ANGPT4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V10, binary
                  cls
clus                 0   1
  ANGPT4 MUTATED     0  11
  ANGPT4 WILD-TYPE  20 449
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANGPT4 MUTATED      0   11
  ANGPT4 WILD-TYPE   20  449
     clus
vv    ANGPT4 MUTATED ANGPT4 WILD-TYPE
  NO               0               20
  YES             11              449
[1] 2 2
[1] FALSE
D344V11, continuous
D344V12, continuous
                  vv
clus                R0  R1  R2  RX
  ANGPT4 MUTATED     6   0   0   1
  ANGPT4 WILD-TYPE 304  11   4  24
D344V13, multiclass
    clus
vv   ANGPT4 MUTATED ANGPT4 WILD-TYPE
  R0              6              304
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANGPT4 MUTATED                                  0     0
  ANGPT4 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANGPT4 MUTATED                           0     9
  ANGPT4 WILD-TYPE                        29   368
D344V14, multiclass
                                  clus
vv                                 ANGPT4 MUTATED ANGPT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V15, binary
                  cls
clus                 0   1
  ANGPT4 MUTATED     2   7
  ANGPT4 WILD-TYPE   4 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANGPT4 MUTATED      2    7
  ANGPT4 WILD-TYPE    4  342
                        clus
vv                       ANGPT4 MUTATED ANGPT4 WILD-TYPE
  HISPANIC OR LATINO                  2                4
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(345) Variable = C12ORF71 MUTATION ANALYSIS
D345V1, survival
                    sevent
clus2                  0   1
  C12ORF71 MUTATED     5   3
  C12ORF71 WILD-TYPE 310 138
  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
                 8                448 
  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
                 3                138 
$`C12ORF71 MUTATED`
TCGA-05-4382 TCGA-44-3918 TCGA-55-6968 TCGA-55-8514 TCGA-55-A494 TCGA-86-7711 
       19.96        34.06        42.51         6.64        15.81        34.39 
TCGA-91-6829 TCGA-95-7947 
       41.36        15.68 

$`C12ORF71 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.30         0.10         4.80        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        20.58        19.59         0.92        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
       13.32        17.62        13.64        26.47        10.62         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
              6.64               0.00 
  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
             42.51             223.96 
  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
             27.01              17.95 
[1] "6.6 - 42.5 (27.0)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D345V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C12ORF71 MUTATED         0        2        4         1         0          0
  C12ORF71 WILD-TYPE       4      121      129        45        67         70
                    vv
clus                 STAGE IIIB STAGE IV
  C12ORF71 MUTATED            0        1
  C12ORF71 WILD-TYPE         11       24
D345V3, multiclass
            clus
vv           C12ORF71 MUTATED C12ORF71 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  2                121
  STAGE IB                  4                129
  STAGE IIA                 1                 45
  STAGE IIB                 0                 67
  STAGE IIIA                0                 70
  STAGE IIIB                0                 11
  STAGE IV                  1                 24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF71 MUTATED     3   5   0   0
  C12ORF71 WILD-TYPE 152 256  43  18
D345V4, multiclass
    clus
vv   C12ORF71 MUTATED C12ORF71 WILD-TYPE
  T1                3                152
  T2                5                256
  T3                0                 43
  T4                0                 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"
                    vv
clus                  N0  N1 N2+N3
  C12ORF71 MUTATED     7   1     0
  C12ORF71 WILD-TYPE 300  88    72
D345V5, multiclass
       clus
vv      C12ORF71 MUTATED C12ORF71 WILD-TYPE
  N0                   7                300
  N1                   1                 88
  N2+N3                0                 72
[1] 3 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
  C12ORF71 MUTATED     4   1
  C12ORF71 WILD-TYPE 323  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF71 MUTATED      4    1
  C12ORF71 WILD-TYPE  323   22
   clus
vv  C12ORF71 MUTATED C12ORF71 WILD-TYPE
  0                4                323
  1                1                 22
[1] 2 2
[1] FALSE
D345V7, binary
                    cls
clus                   0   1
  C12ORF71 MUTATED     3   5
  C12ORF71 WILD-TYPE 256 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF71 MUTATED      3    5
  C12ORF71 WILD-TYPE  256  216
        clus
vv       C12ORF71 MUTATED C12ORF71 WILD-TYPE
  FEMALE                3                256
  MALE                  5                216
[1] 2 2
[1] FALSE
D345V8, continuous
[1] "Remove cluster labels:" "C12ORF71 MUTATED"      
clus
  C12ORF71 MUTATED C12ORF71 WILD-TYPE 
                 2                 82 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-7283         TCGA-55-7573 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-55-7725         TCGA-55-7910         TCGA-55-7914 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8096         TCGA-55-8205 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8507         TCGA-55-8508 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-55-8511         TCGA-55-8512         TCGA-55-8619 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-55-8620         TCGA-55-A48Z         TCGA-55-A490 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-62-8394         TCGA-62-8395         TCGA-62-8397 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-62-8398         TCGA-62-8399         TCGA-62-8402 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-62-A46O         TCGA-62-A46P         TCGA-62-A46R 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-62-A46S         TCGA-62-A46U         TCGA-62-A46V 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-62-A46Y         TCGA-62-A470         TCGA-62-A471 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-62-A472         TCGA-64-1677         TCGA-64-1681 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-64-5778         TCGA-69-7974         TCGA-69-8254 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-71-6725         TCGA-71-8520         TCGA-73-4659 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-73-4662         TCGA-73-4666         TCGA-73-4668 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-73-4676         TCGA-73-7498         TCGA-73-7499 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-75-5122         TCGA-83-5908         TCGA-86-7701 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-86-7713         TCGA-86-7714         TCGA-86-7954 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-86-7955         TCGA-86-8055         TCGA-86-8056 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-86-8074         TCGA-86-8075         TCGA-86-8076 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-86-8278         TCGA-86-8279         TCGA-86-8281 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-86-8358         TCGA-86-8359         TCGA-86-8668 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-86-8669         TCGA-86-8671         TCGA-86-A4JF 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-86-A4P7         TCGA-91-6849         TCGA-93-7348 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-93-8067         TCGA-93-A4JN         TCGA-93-A4JO 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-99-7458         TCGA-MN-A4N1         TCGA-MN-A4N4 
"C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" "C12ORF71 WILD-TYPE" 
        TCGA-MN-A4N5 
"C12ORF71 WILD-TYPE" 
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  C12ORF71 MUTATED                            0
  C12ORF71 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  C12ORF71 MUTATED                                   2
  C12ORF71 WILD-TYPE                               100
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C12ORF71 MUTATED                                                    5
  C12ORF71 WILD-TYPE                                                289
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C12ORF71 MUTATED                                            0
  C12ORF71 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C12ORF71 MUTATED                                               1
  C12ORF71 WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  C12ORF71 MUTATED                                0
  C12ORF71 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  C12ORF71 MUTATED                                    0
  C12ORF71 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C12ORF71 MUTATED                              0                             0
  C12ORF71 WILD-TYPE                            2                            22
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C12ORF71 MUTATED                                               0
  C12ORF71 WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  C12ORF71 MUTATED                              0
  C12ORF71 WILD-TYPE                            9
D345V9, multiclass
                                                    clus
vv                                                   C12ORF71 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   C12ORF71 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V10, binary
                    cls
clus                   0   1
  C12ORF71 MUTATED     0   8
  C12ORF71 WILD-TYPE  20 452
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF71 MUTATED      0    8
  C12ORF71 WILD-TYPE   20  452
     clus
vv    C12ORF71 MUTATED C12ORF71 WILD-TYPE
  NO                 0                 20
  YES                8                452
[1] 2 2
[1] FALSE
D345V11, continuous
D345V12, continuous
                    vv
clus                  R0  R1  R2  RX
  C12ORF71 MUTATED     7   0   0   0
  C12ORF71 WILD-TYPE 303  11   4  25
D345V13, multiclass
    clus
vv   C12ORF71 MUTATED C12ORF71 WILD-TYPE
  R0                7                303
  R1                0                 11
  R2                0                  4
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF71 MUTATED                                  0     0
  C12ORF71 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF71 MUTATED                           1     6
  C12ORF71 WILD-TYPE                        28   371
D345V14, multiclass
                                  clus
vv                                 C12ORF71 MUTATED C12ORF71 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       1                 28
  WHITE                                           6                371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V15, binary
                    cls
clus                   0   1
  C12ORF71 MUTATED     1   6
  C12ORF71 WILD-TYPE   5 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF71 MUTATED      1    6
  C12ORF71 WILD-TYPE    5  343
                        clus
vv                       C12ORF71 MUTATED C12ORF71 WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO                6                343
[1] 2 2
[1] FALSE

Clustering(346) Variable = CAPG MUTATION ANALYSIS
D346V1, survival
                sevent
clus2              0   1
  CAPG MUTATED     3   3
  CAPG WILD-TYPE 312 138
  CAPG MUTATED CAPG WILD-TYPE 
             6            450 
  CAPG MUTATED CAPG WILD-TYPE 
             3            138 
$`CAPG MUTATED`
TCGA-44-A4SS TCGA-50-5930 TCGA-55-A490 TCGA-62-8399 TCGA-64-5775 TCGA-MP-A4TI 
       13.64         9.27         1.58        88.64         2.04        14.10 

$`CAPG WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.08        11.54        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       20.65        55.43        38.37        87.98        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  CAPG MUTATED CAPG WILD-TYPE 
          1.58           0.00 
  CAPG MUTATED CAPG WILD-TYPE 
         88.64         223.96 
  CAPG MUTATED CAPG WILD-TYPE 
        11.455         18.150 
[1] "1.6 - 88.6 (11.5)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D346V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CAPG MUTATED         0        1        0         2         0          3
  CAPG WILD-TYPE       4      122      133        44        67         67
                vv
clus             STAGE IIIB STAGE IV
  CAPG MUTATED            0        0
  CAPG WILD-TYPE         11       25
D346V3, multiclass
            clus
vv           CAPG MUTATED CAPG WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              0            133
  STAGE IIA             2             44
  STAGE IIB             0             67
  STAGE IIIA            3             67
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CAPG MUTATED     1   4   0   1
  CAPG WILD-TYPE 154 257  43  17
D346V4, multiclass
    clus
vv   CAPG MUTATED CAPG WILD-TYPE
  T1            1            154
  T2            4            257
  T3            0             43
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  CAPG MUTATED     3   1     2
  CAPG WILD-TYPE 304  88    70
D346V5, multiclass
       clus
vv      CAPG MUTATED CAPG WILD-TYPE
  N0               3            304
  N1               1             88
  N2+N3            2             70
[1] 3 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
  CAPG MUTATED     5   0
  CAPG WILD-TYPE 322  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  CAPG MUTATED      5    0
  CAPG WILD-TYPE  322   23
   clus
vv  CAPG MUTATED CAPG WILD-TYPE
  0            5            322
  1            0             23
[1] 2 2
[1] FALSE
D346V7, binary
                cls
clus               0   1
  CAPG MUTATED     0   6
  CAPG WILD-TYPE 259 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  CAPG MUTATED      0    6
  CAPG WILD-TYPE  259  215
        clus
vv       CAPG MUTATED CAPG WILD-TYPE
  FEMALE            0            259
  MALE              6            215
[1] 2 2
[1] FALSE
D346V8, continuous
[1] "Remove cluster labels:" "CAPG MUTATED"          
clus
  CAPG MUTATED CAPG WILD-TYPE 
             2             82 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5778     TCGA-69-7974 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-69-8254     TCGA-71-6725     TCGA-71-8520     TCGA-73-4659 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4676 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8055     TCGA-86-8056 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A4JF 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348     TCGA-93-8067 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N1 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" "CAPG WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5 
"CAPG WILD-TYPE" "CAPG WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CAPG MUTATED                            0                                 1
  CAPG WILD-TYPE                         18                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CAPG MUTATED                                                    4
  CAPG WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CAPG MUTATED                                            0
  CAPG WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CAPG MUTATED                                               0
  CAPG WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  CAPG MUTATED                                0
  CAPG WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  CAPG MUTATED                                    0
  CAPG WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CAPG MUTATED                              0                             1
  CAPG WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CAPG MUTATED                                               0
  CAPG WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  CAPG MUTATED                              0
  CAPG WILD-TYPE                            9
D346V9, multiclass
                                                    clus
vv                                                   CAPG MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   CAPG WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V10, binary
                cls
clus               0   1
  CAPG MUTATED     1   5
  CAPG WILD-TYPE  19 455
[1] "tbl2"
                cls
clus             [,1] [,2]
  CAPG MUTATED      1    5
  CAPG WILD-TYPE   19  455
     clus
vv    CAPG MUTATED CAPG WILD-TYPE
  NO             1             19
  YES            5            455
[1] 2 2
[1] FALSE
D346V11, continuous
D346V12, continuous
                vv
clus              R0  R1  R2  RX
  CAPG MUTATED     4   0   0   0
  CAPG WILD-TYPE 306  11   4  25
D346V13, multiclass
    clus
vv   CAPG MUTATED CAPG WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPG MUTATED                                  0     0
  CAPG WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CAPG MUTATED                           0     6
  CAPG WILD-TYPE                        29   371
D346V14, multiclass
                                  clus
vv                                 CAPG MUTATED CAPG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       6            371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V15, binary
                cls
clus               0   1
  CAPG MUTATED     0   6
  CAPG WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  CAPG MUTATED      0    6
  CAPG WILD-TYPE    6  343
                        clus
vv                       CAPG MUTATED CAPG WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(347) Variable = PCDHGA6 MUTATION ANALYSIS
D347V1, survival
                   sevent
clus2                 0   1
  PCDHGA6 MUTATED    16   8
  PCDHGA6 WILD-TYPE 299 133
  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE 
               24               432 
  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE 
                8               133 
$`PCDHGA6 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4434 TCGA-05-5423 TCGA-38-4631 TCGA-38-4632 
       19.96        14.01        15.02         4.96        11.64        44.61 
TCGA-44-6145 TCGA-44-7670 TCGA-44-8120 TCGA-44-A4SU TCGA-53-7624 TCGA-55-6968 
       10.78        29.00         8.55        13.45        34.29        42.51 
TCGA-55-7727 TCGA-55-8092 TCGA-55-8208 TCGA-55-A4DG TCGA-86-7701 TCGA-86-7713 
        1.12         5.06        22.16        19.99        31.13        13.87 
TCGA-86-8054 TCGA-86-8358 TCGA-86-8673 TCGA-97-8179 TCGA-MP-A4TF TCGA-NJ-A4YQ 
       24.49        21.47        14.96        14.30        11.05        29.13 

$`PCDHGA6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       35.28        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 
       26.56        33.30        28.37        12.59        23.77         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        17.59        23.64        12.66         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07        32.65         0.79        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
        3.29        19.66        19.73         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51         2.17        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       20.19         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       34.39        20.55        19.43        19.89        16.70         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
       27.58         0.62        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE 
             1.12              0.00 
  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE 
            44.61            223.96 
  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE 
            14.99             18.10 
[1] "1.1 - 44.6 (15.0)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.5"
D347V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PCDHGA6 MUTATED         0        6        6         3         3          3
  PCDHGA6 WILD-TYPE       4      117      127        43        64         67
                   vv
clus                STAGE IIIB STAGE IV
  PCDHGA6 MUTATED            0        5
  PCDHGA6 WILD-TYPE         11       20
D347V3, multiclass
            clus
vv           PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 6               117
  STAGE IB                 6               127
  STAGE IIA                3                43
  STAGE IIB                3                64
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 5                20
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PCDHGA6 MUTATED     9  14   2   1
  PCDHGA6 WILD-TYPE 146 247  41  17
D347V4, multiclass
    clus
vv   PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  T1               9               146
  T2              14               247
  T3               2                41
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  PCDHGA6 MUTATED    18   5     3
  PCDHGA6 WILD-TYPE 289  84    69
D347V5, multiclass
       clus
vv      PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  N0                 18               289
  N1                  5                84
  N2+N3               3                69
[1] 3 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
  PCDHGA6 MUTATED    17   5
  PCDHGA6 WILD-TYPE 310  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA6 MUTATED     17    5
  PCDHGA6 WILD-TYPE  310   18
   clus
vv  PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  0              17               310
  1               5                18
[1] 2 2
[1] FALSE
D347V7, binary
                   cls
clus                  0   1
  PCDHGA6 MUTATED    11  15
  PCDHGA6 WILD-TYPE 248 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA6 MUTATED     11   15
  PCDHGA6 WILD-TYPE  248  206
        clus
vv       PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  FEMALE              11               248
  MALE                15               206
[1] 2 2
[1] FALSE
D347V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PCDHGA6 MUTATED                            2
  PCDHGA6 WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PCDHGA6 MUTATED                                   4
  PCDHGA6 WILD-TYPE                                98
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PCDHGA6 MUTATED                                                   18
  PCDHGA6 WILD-TYPE                                                276
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PCDHGA6 MUTATED                                            0
  PCDHGA6 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PCDHGA6 MUTATED                                               1
  PCDHGA6 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  PCDHGA6 MUTATED                                0
  PCDHGA6 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  PCDHGA6 MUTATED                                    0
  PCDHGA6 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PCDHGA6 MUTATED                              0                             1
  PCDHGA6 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PCDHGA6 MUTATED                                               0
  PCDHGA6 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  PCDHGA6 MUTATED                              0
  PCDHGA6 WILD-TYPE                            9
D347V9, multiclass
                                                    clus
vv                                                   PCDHGA6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              18
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   PCDHGA6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V10, binary
                   cls
clus                  0   1
  PCDHGA6 MUTATED     0  26
  PCDHGA6 WILD-TYPE  20 434
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA6 MUTATED      0   26
  PCDHGA6 WILD-TYPE   20  434
     clus
vv    PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  NO                0                20
  YES              26               434
[1] 2 2
[1] FALSE
D347V11, continuous
D347V12, continuous
                   vv
clus                 R0  R1  R2  RX
  PCDHGA6 MUTATED    17   0   2   2
  PCDHGA6 WILD-TYPE 293  11   2  23
D347V13, multiclass
    clus
vv   PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  R0              17               293
  R1               0                11
  R2               2                 2
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGA6 MUTATED                                  0     0
  PCDHGA6 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCDHGA6 MUTATED                           2    18
  PCDHGA6 WILD-TYPE                        27   359
D347V14, multiclass
                                  clus
vv                                 PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         18               359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V15, binary
                   cls
clus                  0   1
  PCDHGA6 MUTATED     2  18
  PCDHGA6 WILD-TYPE   4 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA6 MUTATED      2   18
  PCDHGA6 WILD-TYPE    4  331
                        clus
vv                       PCDHGA6 MUTATED PCDHGA6 WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              18               331
[1] 2 2
[1] FALSE

Clustering(348) Variable = ALPP MUTATION ANALYSIS
D348V1, survival
                sevent
clus2              0   1
  ALPP MUTATED     5   5
  ALPP WILD-TYPE 310 136
  ALPP MUTATED ALPP WILD-TYPE 
            10            446 
  ALPP MUTATED ALPP WILD-TYPE 
             5            136 
$`ALPP MUTATED`
TCGA-05-4395 TCGA-49-4507 TCGA-50-5930 TCGA-55-7995 TCGA-55-8299 TCGA-69-7980 
        0.00         8.81         9.27         0.16        15.42        12.56 
TCGA-69-8255 TCGA-69-A59K TCGA-78-7155 TCGA-86-A4JF 
        4.24         7.04        38.50        17.62 

$`ALPP WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       12.66        35.54        46.72        14.07        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         8.22        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
       19.82        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        22.16         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.42         7.56         6.05         2.30         2.93        14.01 
TCGA-69-8254 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       13.45         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        14.96        13.32        13.32        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ALPP MUTATED ALPP WILD-TYPE 
          0.00           0.07 
  ALPP MUTATED ALPP WILD-TYPE 
         38.50         223.96 
  ALPP MUTATED ALPP WILD-TYPE 
          9.04          18.64 
[1] "0.0 - 38.5 (9.0)"   "0.1 - 224.0 (18.6)"
[1] "hr=" "3.9"
D348V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ALPP MUTATED         1        3        1         0         3          2
  ALPP WILD-TYPE       3      120      132        46        64         68
                vv
clus             STAGE IIIB STAGE IV
  ALPP MUTATED            1        0
  ALPP WILD-TYPE         10       25
D348V3, multiclass
            clus
vv           ALPP MUTATED ALPP WILD-TYPE
  STAGE I               1              3
  STAGE IA              3            120
  STAGE IB              1            132
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            2             68
  STAGE IIIB            1             10
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ALPP MUTATED     4   2   4   1
  ALPP WILD-TYPE 151 259  39  17
D348V4, multiclass
    clus
vv   ALPP MUTATED ALPP WILD-TYPE
  T1            4            151
  T2            2            259
  T3            4             39
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  ALPP MUTATED     8   1     2
  ALPP WILD-TYPE 299  88    70
D348V5, multiclass
       clus
vv      ALPP MUTATED ALPP WILD-TYPE
  N0               8            299
  N1               1             88
  N2+N3            2             70
[1] 3 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
  ALPP MUTATED    10   0
  ALPP WILD-TYPE 317  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALPP MUTATED     10    0
  ALPP WILD-TYPE  317   23
   clus
vv  ALPP MUTATED ALPP WILD-TYPE
  0           10            317
  1            0             23
[1] 2 2
[1] FALSE
D348V7, binary
                cls
clus               0   1
  ALPP MUTATED     5   6
  ALPP WILD-TYPE 254 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALPP MUTATED      5    6
  ALPP WILD-TYPE  254  215
        clus
vv       ALPP MUTATED ALPP WILD-TYPE
  FEMALE            5            254
  MALE              6            215
[1] 2 2
[1] FALSE
D348V8, continuous
[1] "Remove cluster labels:" "ALPP MUTATED"          
clus
  ALPP MUTATED ALPP WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-55-A490     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-73-7498     TCGA-73-7499 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-7701     TCGA-86-7711 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7954     TCGA-86-7955 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8074     TCGA-86-8075 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8281 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"ALPP WILD-TYPE" "ALPP WILD-TYPE" "ALPP WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ALPP MUTATED                            0                                 3
  ALPP WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ALPP MUTATED                                                    7
  ALPP WILD-TYPE                                                287
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ALPP MUTATED                                            0
  ALPP WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ALPP MUTATED                                               0
  ALPP WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  ALPP MUTATED                                0
  ALPP WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  ALPP MUTATED                                    0
  ALPP WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ALPP MUTATED                              0                             0
  ALPP WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ALPP MUTATED                                               1
  ALPP WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  ALPP MUTATED                              0
  ALPP WILD-TYPE                            9
D348V9, multiclass
                                                    clus
vv                                                   ALPP MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   ALPP WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V10, binary
                cls
clus               0   1
  ALPP MUTATED     2   9
  ALPP WILD-TYPE  18 451
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALPP MUTATED      2    9
  ALPP WILD-TYPE   18  451
     clus
vv    ALPP MUTATED ALPP WILD-TYPE
  NO             2             18
  YES            9            451
[1] 2 2
[1] FALSE
D348V11, continuous
D348V12, continuous
                vv
clus              R0  R1  R2  RX
  ALPP MUTATED     7   0   0   0
  ALPP WILD-TYPE 303  11   4  25
D348V13, multiclass
    clus
vv   ALPP MUTATED ALPP WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALPP MUTATED                                  0     0
  ALPP WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALPP MUTATED                           1     8
  ALPP WILD-TYPE                        28   369
D348V14, multiclass
                                  clus
vv                                 ALPP MUTATED ALPP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       8            369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V15, binary
                cls
clus               0   1
  ALPP MUTATED     1   7
  ALPP WILD-TYPE   5 342
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALPP MUTATED      1    7
  ALPP WILD-TYPE    5  342
                        clus
vv                       ALPP MUTATED ALPP WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            7            342
[1] 2 2
[1] FALSE

Clustering(349) Variable = ADCY6 MUTATION ANALYSIS
D349V1, survival
                 sevent
clus2               0   1
  ADCY6 MUTATED     4   0
  ADCY6 WILD-TYPE 311 141
  ADCY6 MUTATED ADCY6 WILD-TYPE 
              4             452 
  ADCY6 MUTATED ADCY6 WILD-TYPE 
              0             141 
$`ADCY6 MUTATED`
TCGA-05-4417 TCGA-44-2656 TCGA-55-1595 TCGA-64-5781 
       14.96        46.98        48.62        51.25 

$`ADCY6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ADCY6 MUTATED ADCY6 WILD-TYPE 
          14.96            0.00 
  ADCY6 MUTATED ADCY6 WILD-TYPE 
          51.25          223.96 
  ADCY6 MUTATED ADCY6 WILD-TYPE 
          47.80           17.95 
[1] "15.0 - 51.2 (47.8)" "0.0 - 224.0 (18.0)"
[1] "hr="     "9300000"
D349V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADCY6 MUTATED         0        1        4         0         0          0
  ADCY6 WILD-TYPE       4      122      129        46        67         70
                 vv
clus              STAGE IIIB STAGE IV
  ADCY6 MUTATED            0        0
  ADCY6 WILD-TYPE         11       25
D349V3, multiclass
            clus
vv           ADCY6 MUTATED ADCY6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             129
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADCY6 MUTATED     1   4   0   0
  ADCY6 WILD-TYPE 154 257  43  18
D349V4, multiclass
    clus
vv   ADCY6 MUTATED ADCY6 WILD-TYPE
  T1             1             154
  T2             4             257
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ADCY6 MUTATED     5   0     0
  ADCY6 WILD-TYPE 302  89    72
D349V5, multiclass
       clus
vv      ADCY6 MUTATED ADCY6 WILD-TYPE
  N0                5             302
  N1                0              89
  N2+N3             0              72
[1] 3 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
  ADCY6 MUTATED     5   0
  ADCY6 WILD-TYPE 322  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY6 MUTATED      5    0
  ADCY6 WILD-TYPE  322   23
   clus
vv  ADCY6 MUTATED ADCY6 WILD-TYPE
  0             5             322
  1             0              23
[1] 2 2
[1] FALSE
D349V7, binary
                 cls
clus                0   1
  ADCY6 MUTATED     4   1
  ADCY6 WILD-TYPE 255 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY6 MUTATED      4    1
  ADCY6 WILD-TYPE  255  220
        clus
vv       ADCY6 MUTATED ADCY6 WILD-TYPE
  FEMALE             4             255
  MALE               1             220
[1] 2 2
[1] FALSE
D349V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADCY6 MUTATED                            0                                 2
  ADCY6 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADCY6 MUTATED                                                    2
  ADCY6 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADCY6 MUTATED                                            0
  ADCY6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADCY6 MUTATED                                               0
  ADCY6 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ADCY6 MUTATED                                1
  ADCY6 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ADCY6 MUTATED                                    0
  ADCY6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADCY6 MUTATED                              0                             0
  ADCY6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADCY6 MUTATED                                               0
  ADCY6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ADCY6 MUTATED                              0
  ADCY6 WILD-TYPE                            9
D349V9, multiclass
                                                    clus
vv                                                   ADCY6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ADCY6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V10, binary
                 cls
clus                0   1
  ADCY6 MUTATED     0   5
  ADCY6 WILD-TYPE  20 455
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY6 MUTATED      0    5
  ADCY6 WILD-TYPE   20  455
     clus
vv    ADCY6 MUTATED ADCY6 WILD-TYPE
  NO              0              20
  YES             5             455
[1] 2 2
[1] FALSE
D349V11, continuous
D349V12, continuous
                 vv
clus               R0  R1  R2  RX
  ADCY6 MUTATED     3   0   0   0
  ADCY6 WILD-TYPE 307  11   4  25
D349V13, multiclass
    clus
vv   ADCY6 MUTATED ADCY6 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADCY6 MUTATED                                  0     1
  ADCY6 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADCY6 MUTATED                           0     2
  ADCY6 WILD-TYPE                        29   375
D349V14, multiclass
                                  clus
vv                                 ADCY6 MUTATED ADCY6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        2             375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V15, binary
                 cls
clus                0   1
  ADCY6 MUTATED     0   3
  ADCY6 WILD-TYPE   6 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY6 MUTATED      0    3
  ADCY6 WILD-TYPE    6  346
                        clus
vv                       ADCY6 MUTATED ADCY6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             346
[1] 2 2
[1] FALSE

Clustering(350) Variable = GOLGA6B MUTATION ANALYSIS
D350V1, survival
                   sevent
clus2                 0   1
  GOLGA6B MUTATED     6   3
  GOLGA6B WILD-TYPE 309 138
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                9               447 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                3               138 
$`GOLGA6B MUTATED`
TCGA-50-5049 TCGA-50-6590 TCGA-55-8302 TCGA-73-7498 TCGA-78-7159 TCGA-78-7220 
       70.55        42.35         0.76        39.09        64.90        26.53 
TCGA-78-7536 TCGA-86-6851 TCGA-86-8073 
        8.02         5.88        24.33 

$`GOLGA6B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       15.35         4.31         1.32         5.39         1.25        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        5.88        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       88.14        31.20        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
             0.76              0.00 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
            70.55            223.96 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
            26.53             17.92 
[1] "0.8 - 70.5 (26.5)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.4"
D350V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GOLGA6B MUTATED         0        3        3         1         0          3
  GOLGA6B WILD-TYPE       4      120      130        45        67         67
                   vv
clus                STAGE IIIB STAGE IV
  GOLGA6B MUTATED            0        0
  GOLGA6B WILD-TYPE         11       25
D350V3, multiclass
            clus
vv           GOLGA6B MUTATED GOLGA6B WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 3               120
  STAGE IB                 3               130
  STAGE IIA                1                45
  STAGE IIB                0                67
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GOLGA6B MUTATED     3   6   1   0
  GOLGA6B WILD-TYPE 152 255  42  18
D350V4, multiclass
    clus
vv   GOLGA6B MUTATED GOLGA6B WILD-TYPE
  T1               3               152
  T2               6               255
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  GOLGA6B MUTATED     5   1     3
  GOLGA6B WILD-TYPE 302  88    69
D350V5, multiclass
       clus
vv      GOLGA6B MUTATED GOLGA6B WILD-TYPE
  N0                  5               302
  N1                  1                88
  N2+N3               3                69
[1] 3 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
  GOLGA6B MUTATED     9   0
  GOLGA6B WILD-TYPE 318  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      9    0
  GOLGA6B WILD-TYPE  318   23
   clus
vv  GOLGA6B MUTATED GOLGA6B WILD-TYPE
  0               9               318
  1               0                23
[1] 2 2
[1] FALSE
D350V7, binary
                   cls
clus                  0   1
  GOLGA6B MUTATED     6   4
  GOLGA6B WILD-TYPE 253 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      6    4
  GOLGA6B WILD-TYPE  253  217
        clus
vv       GOLGA6B MUTATED GOLGA6B WILD-TYPE
  FEMALE               6               253
  MALE                 4               217
[1] 2 2
[1] FALSE
D350V8, continuous
[1] "Remove cluster labels:" "GOLGA6B MUTATED"       
clus
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7499        TCGA-75-5122 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  GOLGA6B MUTATED                            0
  GOLGA6B WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  GOLGA6B MUTATED                                   3
  GOLGA6B WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GOLGA6B MUTATED                                                    4
  GOLGA6B WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GOLGA6B MUTATED                                            0
  GOLGA6B WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GOLGA6B MUTATED                                               2
  GOLGA6B WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  GOLGA6B MUTATED                                0
  GOLGA6B WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  GOLGA6B MUTATED                                    0
  GOLGA6B WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GOLGA6B MUTATED                              0                             1
  GOLGA6B WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GOLGA6B MUTATED                                               0
  GOLGA6B WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  GOLGA6B MUTATED                              0
  GOLGA6B WILD-TYPE                            9
D350V9, multiclass
                                                    clus
vv                                                   GOLGA6B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   GOLGA6B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V10, binary
                   cls
clus                  0   1
  GOLGA6B MUTATED     3   7
  GOLGA6B WILD-TYPE  17 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      3    7
  GOLGA6B WILD-TYPE   17  453
     clus
vv    GOLGA6B MUTATED GOLGA6B WILD-TYPE
  NO                3                17
  YES               7               453
[1] 2 2
[1] FALSE
D350V11, continuous
D350V12, continuous
                   vv
clus                 R0  R1  R2  RX
  GOLGA6B MUTATED     6   0   1   0
  GOLGA6B WILD-TYPE 304  11   3  25
D350V13, multiclass
    clus
vv   GOLGA6B MUTATED GOLGA6B WILD-TYPE
  R0               6               304
  R1               0                11
  R2               1                 3
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLGA6B MUTATED                                  0     0
  GOLGA6B WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GOLGA6B MUTATED                           0     9
  GOLGA6B WILD-TYPE                        29   368
D350V14, multiclass
                                  clus
vv                                 GOLGA6B MUTATED GOLGA6B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          9               368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V15, binary
                   cls
clus                  0   1
  GOLGA6B MUTATED     0   5
  GOLGA6B WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      0    5
  GOLGA6B WILD-TYPE    6  344
                        clus
vv                       GOLGA6B MUTATED GOLGA6B WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(351) Variable = TMEM135 MUTATION ANALYSIS
D351V1, survival
                   sevent
clus2                 0   1
  TMEM135 MUTATED     7   2
  TMEM135 WILD-TYPE 308 139
  TMEM135 MUTATED TMEM135 WILD-TYPE 
                9               447 
  TMEM135 MUTATED TMEM135 WILD-TYPE 
                2               139 
$`TMEM135 MUTATED`
TCGA-05-4382 TCGA-44-6147 TCGA-44-7661 TCGA-44-8117 TCGA-44-8119 TCGA-55-6969 
       19.96        27.78        12.03        12.66         3.25        40.73 
TCGA-78-8640 TCGA-86-8672 TCGA-MP-A4TK 
      214.62         0.62        19.13 

$`TMEM135 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        14.60        19.46         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       29.00        17.59        23.64         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 
        2.86         0.07        32.65         0.79        42.51        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       10.55        32.68        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       30.84        27.58        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
       10.09        29.46        11.05        14.66        14.10        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  TMEM135 MUTATED TMEM135 WILD-TYPE 
             0.62              0.00 
  TMEM135 MUTATED TMEM135 WILD-TYPE 
           214.62            223.96 
  TMEM135 MUTATED TMEM135 WILD-TYPE 
            19.13             17.98 
[1] "0.6 - 214.6 (19.1)" "0.0 - 224.0 (18.0)"
[1] "hr=" "2"  
D351V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TMEM135 MUTATED         0        1        4         1         3          0
  TMEM135 WILD-TYPE       4      122      129        45        64         70
                   vv
clus                STAGE IIIB STAGE IV
  TMEM135 MUTATED            0        0
  TMEM135 WILD-TYPE         11       25
D351V3, multiclass
            clus
vv           TMEM135 MUTATED TMEM135 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 4               129
  STAGE IIA                1                45
  STAGE IIB                3                64
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM135 MUTATED     2   5   2   0
  TMEM135 WILD-TYPE 153 256  41  18
D351V4, multiclass
    clus
vv   TMEM135 MUTATED TMEM135 WILD-TYPE
  T1               2               153
  T2               5               256
  T3               2                41
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  TMEM135 MUTATED     6   2     0
  TMEM135 WILD-TYPE 301  87    72
D351V5, multiclass
       clus
vv      TMEM135 MUTATED TMEM135 WILD-TYPE
  N0                  6               301
  N1                  2                87
  N2+N3               0                72
[1] 3 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
  TMEM135 MUTATED     8   0
  TMEM135 WILD-TYPE 319  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM135 MUTATED      8    0
  TMEM135 WILD-TYPE  319   23
   clus
vv  TMEM135 MUTATED TMEM135 WILD-TYPE
  0               8               319
  1               0                23
[1] 2 2
[1] FALSE
D351V7, binary
                   cls
clus                  0   1
  TMEM135 MUTATED     4   5
  TMEM135 WILD-TYPE 255 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM135 MUTATED      4    5
  TMEM135 WILD-TYPE  255  216
        clus
vv       TMEM135 MUTATED TMEM135 WILD-TYPE
  FEMALE               4               255
  MALE                 5               216
[1] 2 2
[1] FALSE
D351V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  TMEM135 MUTATED                            0
  TMEM135 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  TMEM135 MUTATED                                   1
  TMEM135 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TMEM135 MUTATED                                                    8
  TMEM135 WILD-TYPE                                                286
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TMEM135 MUTATED                                            0
  TMEM135 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TMEM135 MUTATED                                               0
  TMEM135 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  TMEM135 MUTATED                                0
  TMEM135 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  TMEM135 MUTATED                                    0
  TMEM135 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TMEM135 MUTATED                              0                             0
  TMEM135 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TMEM135 MUTATED                                               0
  TMEM135 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  TMEM135 MUTATED                              0
  TMEM135 WILD-TYPE                            9
D351V9, multiclass
                                                    clus
vv                                                   TMEM135 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   TMEM135 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V10, binary
                   cls
clus                  0   1
  TMEM135 MUTATED     0   9
  TMEM135 WILD-TYPE  20 451
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM135 MUTATED      0    9
  TMEM135 WILD-TYPE   20  451
     clus
vv    TMEM135 MUTATED TMEM135 WILD-TYPE
  NO                0                20
  YES               9               451
[1] 2 2
[1] FALSE
D351V11, continuous
D351V12, continuous
                   vv
clus                 R0  R1  R2  RX
  TMEM135 MUTATED     4   0   0   0
  TMEM135 WILD-TYPE 306  11   4  25
D351V13, multiclass
    clus
vv   TMEM135 MUTATED TMEM135 WILD-TYPE
  R0               4               306
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM135 MUTATED                                  0     0
  TMEM135 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM135 MUTATED                           0     6
  TMEM135 WILD-TYPE                        29   371
D351V14, multiclass
                                  clus
vv                                 TMEM135 MUTATED TMEM135 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V15, binary
                   cls
clus                  0   1
  TMEM135 MUTATED     0   5
  TMEM135 WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM135 MUTATED      0    5
  TMEM135 WILD-TYPE    6  344
                        clus
vv                       TMEM135 MUTATED TMEM135 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(352) Variable = MSR1 MUTATION ANALYSIS
D352V1, survival
                sevent
clus2              0   1
  MSR1 MUTATED     6   1
  MSR1 WILD-TYPE 309 140
  MSR1 MUTATED MSR1 WILD-TYPE 
             7            449 
  MSR1 MUTATED MSR1 WILD-TYPE 
             1            140 
$`MSR1 MUTATED`
TCGA-44-3398 TCGA-78-8662 TCGA-86-6851 TCGA-86-8073 TCGA-86-8674 TCGA-91-A4BC 
       38.24       110.50         5.88        24.33        13.32         1.45 
TCGA-95-A4VN 
       18.18 

$`MSR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       32.68       214.62        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.18        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  MSR1 MUTATED MSR1 WILD-TYPE 
          1.45           0.00 
  MSR1 MUTATED MSR1 WILD-TYPE 
        110.50         223.96 
  MSR1 MUTATED MSR1 WILD-TYPE 
         18.18          17.98 
[1] "1.4 - 110.5 (18.2)" "0.0 - 224.0 (18.0)"
[1] "hr=" "3.2"
D352V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MSR1 MUTATED         0        1        2         4         0          0
  MSR1 WILD-TYPE       4      122      131        42        67         70
                vv
clus             STAGE IIIB STAGE IV
  MSR1 MUTATED            0        0
  MSR1 WILD-TYPE         11       25
D352V3, multiclass
            clus
vv           MSR1 MUTATED MSR1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            131
  STAGE IIA             4             42
  STAGE IIB             0             67
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSR1 MUTATED     2   5   0   0
  MSR1 WILD-TYPE 153 256  43  18
D352V4, multiclass
    clus
vv   MSR1 MUTATED MSR1 WILD-TYPE
  T1            2            153
  T2            5            256
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  MSR1 MUTATED     4   3     0
  MSR1 WILD-TYPE 303  86    72
D352V5, multiclass
       clus
vv      MSR1 MUTATED MSR1 WILD-TYPE
  N0               4            303
  N1               3             86
  N2+N3            0             72
[1] 3 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
  MSR1 MUTATED     6   0
  MSR1 WILD-TYPE 321  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSR1 MUTATED      6    0
  MSR1 WILD-TYPE  321   23
   clus
vv  MSR1 MUTATED MSR1 WILD-TYPE
  0            6            321
  1            0             23
[1] 2 2
[1] FALSE
D352V7, binary
                cls
clus               0   1
  MSR1 MUTATED     4   3
  MSR1 WILD-TYPE 255 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSR1 MUTATED      4    3
  MSR1 WILD-TYPE  255  218
        clus
vv       MSR1 MUTATED MSR1 WILD-TYPE
  FEMALE            4            255
  MALE              3            218
[1] 2 2
[1] FALSE
D352V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MSR1 MUTATED                            0                                 1
  MSR1 WILD-TYPE                         18                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MSR1 MUTATED                                                    3
  MSR1 WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MSR1 MUTATED                                            0
  MSR1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MSR1 MUTATED                                               1
  MSR1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MSR1 MUTATED                                0
  MSR1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MSR1 MUTATED                                    0
  MSR1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MSR1 MUTATED                              0                             1
  MSR1 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MSR1 MUTATED                                               1
  MSR1 WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MSR1 MUTATED                              0
  MSR1 WILD-TYPE                            9
D352V9, multiclass
                                                    clus
vv                                                   MSR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MSR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V10, binary
                cls
clus               0   1
  MSR1 MUTATED     0   7
  MSR1 WILD-TYPE  20 453
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSR1 MUTATED      0    7
  MSR1 WILD-TYPE   20  453
     clus
vv    MSR1 MUTATED MSR1 WILD-TYPE
  NO             0             20
  YES            7            453
[1] 2 2
[1] FALSE
D352V11, continuous
D352V12, continuous
                vv
clus              R0  R1  R2  RX
  MSR1 MUTATED     5   0   0   0
  MSR1 WILD-TYPE 305  11   4  25
D352V13, multiclass
    clus
vv   MSR1 MUTATED MSR1 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSR1 MUTATED                                  0     0
  MSR1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSR1 MUTATED                           0     6
  MSR1 WILD-TYPE                        29   371
D352V14, multiclass
                                  clus
vv                                 MSR1 MUTATED MSR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       6            371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V15, binary
                cls
clus               0   1
  MSR1 MUTATED     0   6
  MSR1 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSR1 MUTATED      0    6
  MSR1 WILD-TYPE    6  343
                        clus
vv                       MSR1 MUTATED MSR1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(353) Variable = ZNF768 MUTATION ANALYSIS
D353V1, survival
                  sevent
clus2                0   1
  ZNF768 MUTATED     5   3
  ZNF768 WILD-TYPE 310 138
  ZNF768 MUTATED ZNF768 WILD-TYPE 
               8              448 
  ZNF768 MUTATED ZNF768 WILD-TYPE 
               3              138 
$`ZNF768 MUTATED`
TCGA-50-5941 TCGA-50-6590 TCGA-55-8208 TCGA-55-8511 TCGA-78-8660 TCGA-95-7947 
       18.64        42.35        22.16         0.30        10.55        15.68 
TCGA-97-8174 TCGA-99-8032 
        5.39         1.45 

$`ZNF768 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       15.12        29.03        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51         2.17        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ZNF768 MUTATED ZNF768 WILD-TYPE 
             0.3              0.0 
  ZNF768 MUTATED ZNF768 WILD-TYPE 
           42.35           223.96 
  ZNF768 MUTATED ZNF768 WILD-TYPE 
          13.115           18.100 
[1] "0.3 - 42.4 (13.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.1"
D353V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF768 MUTATED         0        3        2         1         1          1
  ZNF768 WILD-TYPE       4      120      131        45        66         69
                  vv
clus               STAGE IIIB STAGE IV
  ZNF768 MUTATED            0        0
  ZNF768 WILD-TYPE         11       25
D353V3, multiclass
            clus
vv           ZNF768 MUTATED ZNF768 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                2              131
  STAGE IIA               1               45
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF768 MUTATED     3   5   0   0
  ZNF768 WILD-TYPE 152 256  43  18
D353V4, multiclass
    clus
vv   ZNF768 MUTATED ZNF768 WILD-TYPE
  T1              3              152
  T2              5              256
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ZNF768 MUTATED     6   1     1
  ZNF768 WILD-TYPE 301  88    71
D353V5, multiclass
       clus
vv      ZNF768 MUTATED ZNF768 WILD-TYPE
  N0                 6              301
  N1                 1               88
  N2+N3              1               71
[1] 3 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
  ZNF768 MUTATED     7   0
  ZNF768 WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF768 MUTATED      7    0
  ZNF768 WILD-TYPE  320   23
   clus
vv  ZNF768 MUTATED ZNF768 WILD-TYPE
  0              7              320
  1              0               23
[1] 2 2
[1] FALSE
D353V7, binary
                  cls
clus                 0   1
  ZNF768 MUTATED     4   4
  ZNF768 WILD-TYPE 255 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF768 MUTATED      4    4
  ZNF768 WILD-TYPE  255  217
        clus
vv       ZNF768 MUTATED ZNF768 WILD-TYPE
  FEMALE              4              255
  MALE                4              217
[1] 2 2
[1] FALSE
D353V8, continuous
[1] "Remove cluster labels:" "ZNF768 MUTATED"        
clus
  ZNF768 MUTATED ZNF768 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8512       TCGA-55-8619 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5778       TCGA-69-7974 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4676 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"ZNF768 WILD-TYPE" "ZNF768 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF768 MUTATED                            0                                 1
  ZNF768 WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF768 MUTATED                                                    6
  ZNF768 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF768 MUTATED                                            0
  ZNF768 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF768 MUTATED                                               0
  ZNF768 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF768 MUTATED                                0
  ZNF768 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF768 MUTATED                                    0
  ZNF768 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF768 MUTATED                              0                             1
  ZNF768 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF768 MUTATED                                               0
  ZNF768 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF768 MUTATED                              0
  ZNF768 WILD-TYPE                            9
D353V9, multiclass
                                                    clus
vv                                                   ZNF768 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF768 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V10, binary
                  cls
clus                 0   1
  ZNF768 MUTATED     0   8
  ZNF768 WILD-TYPE  20 452
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF768 MUTATED      0    8
  ZNF768 WILD-TYPE   20  452
     clus
vv    ZNF768 MUTATED ZNF768 WILD-TYPE
  NO               0               20
  YES              8              452
[1] 2 2
[1] FALSE
D353V11, continuous
D353V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF768 MUTATED     5   0   0   0
  ZNF768 WILD-TYPE 305  11   4  25
D353V13, multiclass
    clus
vv   ZNF768 MUTATED ZNF768 WILD-TYPE
  R0              5              305
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF768 MUTATED                                  0     0
  ZNF768 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF768 MUTATED                           0     7
  ZNF768 WILD-TYPE                        29   370
D353V14, multiclass
                                  clus
vv                                 ZNF768 MUTATED ZNF768 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V15, binary
                  cls
clus                 0   1
  ZNF768 MUTATED     0   6
  ZNF768 WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF768 MUTATED      0    6
  ZNF768 WILD-TYPE    6  343
                        clus
vv                       ZNF768 MUTATED ZNF768 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              343
[1] 2 2
[1] FALSE

Clustering(354) Variable = UNC93A MUTATION ANALYSIS
D354V1, survival
                  sevent
clus2                0   1
  UNC93A MUTATED     7   2
  UNC93A WILD-TYPE 308 139
  UNC93A MUTATED UNC93A WILD-TYPE 
               9              447 
  UNC93A MUTATED UNC93A WILD-TYPE 
               2              139 
$`UNC93A MUTATED`
TCGA-05-4382 TCGA-38-4625 TCGA-44-7670 TCGA-55-7907 TCGA-64-5781 TCGA-78-7148 
       19.96        97.74        29.00         0.53        51.25        20.58 
TCGA-78-7152 TCGA-78-8662 TCGA-86-8358 
       39.52       110.50        21.47 

$`UNC93A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
       27.16         5.69        19.27        35.93        21.90        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       32.68       214.62        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  UNC93A MUTATED UNC93A WILD-TYPE 
            0.53             0.00 
  UNC93A MUTATED UNC93A WILD-TYPE 
          110.50           223.96 
  UNC93A MUTATED UNC93A WILD-TYPE 
           29.00            17.72 
[1] "0.5 - 110.5 (29.0)" "0.0 - 224.0 (17.7)"
[1] "hr=" "3.1"
D354V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  UNC93A MUTATED         0        0        6         2         1          0
  UNC93A WILD-TYPE       4      123      127        44        66         70
                  vv
clus               STAGE IIIB STAGE IV
  UNC93A MUTATED            0        0
  UNC93A WILD-TYPE         11       25
D354V3, multiclass
            clus
vv           UNC93A MUTATED UNC93A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0              123
  STAGE IB                6              127
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UNC93A MUTATED     1   8   0   0
  UNC93A WILD-TYPE 154 253  43  18
D354V4, multiclass
    clus
vv   UNC93A MUTATED UNC93A WILD-TYPE
  T1              1              154
  T2              8              253
  T3              0               43
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  UNC93A MUTATED     6   3     0
  UNC93A WILD-TYPE 301  86    72
D354V5, multiclass
       clus
vv      UNC93A MUTATED UNC93A WILD-TYPE
  N0                 6              301
  N1                 3               86
  N2+N3              0               72
[1] 3 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
  UNC93A MUTATED     8   0
  UNC93A WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UNC93A MUTATED      8    0
  UNC93A WILD-TYPE  319   23
   clus
vv  UNC93A MUTATED UNC93A WILD-TYPE
  0              8              319
  1              0               23
[1] 2 2
[1] FALSE
D354V7, binary
                  cls
clus                 0   1
  UNC93A MUTATED     4   5
  UNC93A WILD-TYPE 255 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UNC93A MUTATED      4    5
  UNC93A WILD-TYPE  255  216
        clus
vv       UNC93A MUTATED UNC93A WILD-TYPE
  FEMALE              4              255
  MALE                5              216
[1] 2 2
[1] FALSE
D354V8, continuous
[1] "Remove cluster labels:" "UNC93A MUTATED"        
clus
  UNC93A MUTATED UNC93A WILD-TYPE 
               1               83 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8279       TCGA-86-8281 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"UNC93A WILD-TYPE" "UNC93A WILD-TYPE" "UNC93A WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  UNC93A MUTATED                            0                                 4
  UNC93A WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  UNC93A MUTATED                                                    5
  UNC93A WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  UNC93A MUTATED                                            0
  UNC93A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  UNC93A MUTATED                                               0
  UNC93A WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  UNC93A MUTATED                                0
  UNC93A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  UNC93A MUTATED                                    0
  UNC93A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  UNC93A MUTATED                              0                             0
  UNC93A WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  UNC93A MUTATED                                               0
  UNC93A WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  UNC93A MUTATED                              0
  UNC93A WILD-TYPE                            9
D354V9, multiclass
                                                    clus
vv                                                   UNC93A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   UNC93A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V10, binary
                  cls
clus                 0   1
  UNC93A MUTATED     0   9
  UNC93A WILD-TYPE  20 451
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UNC93A MUTATED      0    9
  UNC93A WILD-TYPE   20  451
     clus
vv    UNC93A MUTATED UNC93A WILD-TYPE
  NO               0               20
  YES              9              451
[1] 2 2
[1] FALSE
D354V11, continuous
D354V12, continuous
                  vv
clus                R0  R1  R2  RX
  UNC93A MUTATED     8   0   0   0
  UNC93A WILD-TYPE 302  11   4  25
D354V13, multiclass
    clus
vv   UNC93A MUTATED UNC93A WILD-TYPE
  R0              8              302
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UNC93A MUTATED                                  0     0
  UNC93A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UNC93A MUTATED                           0     7
  UNC93A WILD-TYPE                        29   370
D354V14, multiclass
                                  clus
vv                                 UNC93A MUTATED UNC93A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V15, binary
                  cls
clus                 0   1
  UNC93A MUTATED     1   4
  UNC93A WILD-TYPE   5 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UNC93A MUTATED      1    4
  UNC93A WILD-TYPE    5  345
                        clus
vv                       UNC93A MUTATED UNC93A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(355) Variable = CACNA2D4 MUTATION ANALYSIS
D355V1, survival
                    sevent
clus2                  0   1
  CACNA2D4 MUTATED    15   8
  CACNA2D4 WILD-TYPE 300 133
  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE 
                23                433 
  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE 
                 8                133 
$`CACNA2D4 MUTATED`
TCGA-05-4390 TCGA-44-3398 TCGA-50-5049 TCGA-50-6594 TCGA-55-6979 TCGA-55-8085 
       37.02        38.24        70.55        12.16         7.79        29.72 
TCGA-55-8089 TCGA-55-8510 TCGA-55-8511 TCGA-55-8620 TCGA-55-A4DF TCGA-62-A46P 
        3.29        17.72         0.30         2.17        20.19        19.53 
TCGA-64-5775 TCGA-78-8662 TCGA-86-7955 TCGA-86-8073 TCGA-86-8585 TCGA-86-A4P7 
        2.04       110.50        16.70        24.33         1.15        13.64 
TCGA-91-7771 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TA TCGA-NJ-A55A 
       16.18        38.63        86.14        31.23         0.26 

$`CACNA2D4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.49         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
        1.58        20.58        19.59         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       47.80        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       32.68       214.62        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.43        19.89        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        17.62        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        7.36         1.15        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64        29.13         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE 
              0.26               0.00 
  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE 
            110.50             223.96 
  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE 
             17.72              18.08 
[1] "0.3 - 110.5 (17.7)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D355V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CACNA2D4 MUTATED         0        7       11         0         2          2
  CACNA2D4 WILD-TYPE       4      116      122        46        65         68
                    vv
clus                 STAGE IIIB STAGE IV
  CACNA2D4 MUTATED            0        1
  CACNA2D4 WILD-TYPE         11       24
D355V3, multiclass
            clus
vv           CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  7                116
  STAGE IB                 11                122
  STAGE IIA                 0                 46
  STAGE IIB                 2                 65
  STAGE IIIA                2                 68
  STAGE IIIB                0                 11
  STAGE IV                  1                 24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CACNA2D4 MUTATED     7  13   2   1
  CACNA2D4 WILD-TYPE 148 248  41  17
D355V4, multiclass
    clus
vv   CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  T1                7                148
  T2               13                248
  T3                2                 41
  T4                1                 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"
                    vv
clus                  N0  N1 N2+N3
  CACNA2D4 MUTATED    20   2     1
  CACNA2D4 WILD-TYPE 287  87    71
D355V5, multiclass
       clus
vv      CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  N0                  20                287
  N1                   2                 87
  N2+N3                1                 71
[1] 3 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
  CACNA2D4 MUTATED    18   1
  CACNA2D4 WILD-TYPE 309  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D4 MUTATED     18    1
  CACNA2D4 WILD-TYPE  309   22
   clus
vv  CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  0               18                309
  1                1                 22
[1] 2 2
[1] FALSE
D355V7, binary
                    cls
clus                   0   1
  CACNA2D4 MUTATED    10  13
  CACNA2D4 WILD-TYPE 249 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D4 MUTATED     10   13
  CACNA2D4 WILD-TYPE  249  208
        clus
vv       CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  FEMALE               10                249
  MALE                 13                208
[1] 2 2
[1] FALSE
D355V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  CACNA2D4 MUTATED                            0
  CACNA2D4 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  CACNA2D4 MUTATED                                   2
  CACNA2D4 WILD-TYPE                               100
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CACNA2D4 MUTATED                                                   18
  CACNA2D4 WILD-TYPE                                                276
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CACNA2D4 MUTATED                                            0
  CACNA2D4 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CACNA2D4 MUTATED                                               1
  CACNA2D4 WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  CACNA2D4 MUTATED                                0
  CACNA2D4 WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  CACNA2D4 MUTATED                                    0
  CACNA2D4 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CACNA2D4 MUTATED                              0                             1
  CACNA2D4 WILD-TYPE                            2                            21
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CACNA2D4 MUTATED                                               1
  CACNA2D4 WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  CACNA2D4 MUTATED                              0
  CACNA2D4 WILD-TYPE                            9
D355V9, multiclass
                                                    clus
vv                                                   CACNA2D4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               18
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   CACNA2D4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V10, binary
                    cls
clus                   0   1
  CACNA2D4 MUTATED     1  22
  CACNA2D4 WILD-TYPE  19 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D4 MUTATED      1   22
  CACNA2D4 WILD-TYPE   19  438
     clus
vv    CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  NO                 1                 19
  YES               22                438
[1] 2 2
[1] FALSE
D355V11, continuous
D355V12, continuous
                    vv
clus                  R0  R1  R2  RX
  CACNA2D4 MUTATED    17   0   0   1
  CACNA2D4 WILD-TYPE 293  11   4  24
D355V13, multiclass
    clus
vv   CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  R0               17                293
  R1                0                 11
  R2                0                  4
  RX                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA2D4 MUTATED                                  0     0
  CACNA2D4 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CACNA2D4 MUTATED                           1    19
  CACNA2D4 WILD-TYPE                        28   358
D355V14, multiclass
                                  clus
vv                                 CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       1                 28
  WHITE                                          19                358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V15, binary
                    cls
clus                   0   1
  CACNA2D4 MUTATED     0  19
  CACNA2D4 WILD-TYPE   6 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D4 MUTATED      0   19
  CACNA2D4 WILD-TYPE    6  330
                        clus
vv                       CACNA2D4 MUTATED CACNA2D4 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               19                330
[1] 2 2
[1] FALSE

Clustering(356) Variable = KIRREL MUTATION ANALYSIS
D356V1, survival
                  sevent
clus2                0   1
  KIRREL MUTATED    10   5
  KIRREL WILD-TYPE 305 136
  KIRREL MUTATED KIRREL WILD-TYPE 
              15              441 
  KIRREL MUTATED KIRREL WILD-TYPE 
               5              136 
$`KIRREL MUTATED`
TCGA-05-5428 TCGA-44-5644 TCGA-44-7670 TCGA-50-5930 TCGA-50-5933 TCGA-50-6590 
       22.03        28.37        29.00         9.27        78.67        42.35 
TCGA-55-8506 TCGA-62-A46O TCGA-64-1676 TCGA-64-5781 TCGA-69-7979 TCGA-69-7980 
        0.36        47.80        56.81        51.25         2.93        12.56 
TCGA-78-8662 TCGA-86-A4JF TCGA-99-8025 
      110.50        17.62        34.85 

$`KIRREL WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       24.00        15.02        15.02         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
       31.04        49.28         8.22        14.27        40.60        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 
       13.61         5.42         7.56         6.05         2.30        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        20.68        24.56        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  KIRREL MUTATED KIRREL WILD-TYPE 
            0.36             0.00 
  KIRREL MUTATED KIRREL WILD-TYPE 
          110.50           223.96 
  KIRREL MUTATED KIRREL WILD-TYPE 
           29.00            17.75 
[1] "0.4 - 110.5 (29.0)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.7"
D356V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KIRREL MUTATED         1        1        7         2         2          2
  KIRREL WILD-TYPE       3      122      126        44        65         68
                  vv
clus               STAGE IIIB STAGE IV
  KIRREL MUTATED            1        0
  KIRREL WILD-TYPE         10       25
D356V3, multiclass
            clus
vv           KIRREL MUTATED KIRREL WILD-TYPE
  STAGE I                 1                3
  STAGE IA                1              122
  STAGE IB                7              126
  STAGE IIA               2               44
  STAGE IIB               2               65
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of 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     4   8   3   1
  KIRREL WILD-TYPE 151 253  40  17
D356V4, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  T1              4              151
  T2              8              253
  T3              3               40
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  KIRREL MUTATED    11   2     3
  KIRREL WILD-TYPE 296  87    69
D356V5, multiclass
       clus
vv      KIRREL MUTATED KIRREL WILD-TYPE
  N0                11              296
  N1                 2               87
  N2+N3              3               69
[1] 3 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
  KIRREL MUTATED    13   0
  KIRREL WILD-TYPE 314  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     13    0
  KIRREL WILD-TYPE  314   23
   clus
vv  KIRREL MUTATED KIRREL WILD-TYPE
  0             13              314
  1              0               23
[1] 2 2
[1] FALSE
D356V7, binary
                  cls
clus                 0   1
  KIRREL MUTATED    10   6
  KIRREL WILD-TYPE 249 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     10    6
  KIRREL WILD-TYPE  249  215
        clus
vv       KIRREL MUTATED KIRREL WILD-TYPE
  FEMALE             10              249
  MALE                6              215
[1] 2 2
[1] FALSE
D356V8, continuous
[1] "Remove cluster labels:" "KIRREL MUTATED"        
clus
  KIRREL MUTATED KIRREL WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KIRREL MUTATED                            1                                 4
  KIRREL WILD-TYPE                         17                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KIRREL MUTATED                                                   11
  KIRREL WILD-TYPE                                                283
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KIRREL MUTATED                                            0
  KIRREL WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KIRREL MUTATED                                               0
  KIRREL WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  KIRREL MUTATED                                0
  KIRREL WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  KIRREL MUTATED                                    0
  KIRREL WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KIRREL MUTATED                              0                             0
  KIRREL WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KIRREL MUTATED                                               0
  KIRREL WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  KIRREL MUTATED                              0
  KIRREL WILD-TYPE                            9
D356V9, multiclass
                                                    clus
vv                                                   KIRREL MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   KIRREL WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V10, binary
                  cls
clus                 0   1
  KIRREL MUTATED     2  14
  KIRREL WILD-TYPE  18 446
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      2   14
  KIRREL WILD-TYPE   18  446
     clus
vv    KIRREL MUTATED KIRREL WILD-TYPE
  NO               2               18
  YES             14              446
[1] 2 2
[1] FALSE
D356V11, continuous
D356V12, continuous
                  vv
clus                R0  R1  R2  RX
  KIRREL MUTATED     8   0   0   1
  KIRREL WILD-TYPE 302  11   4  24
D356V13, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  R0              8              302
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIRREL MUTATED                                  0     0
  KIRREL WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIRREL MUTATED                           1    12
  KIRREL WILD-TYPE                        28   365
D356V14, multiclass
                                  clus
vv                                 KIRREL MUTATED KIRREL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        12              365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V15, binary
                  cls
clus                 0   1
  KIRREL MUTATED     1  12
  KIRREL WILD-TYPE   5 337
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      1   12
  KIRREL WILD-TYPE    5  337
                        clus
vv                       KIRREL MUTATED KIRREL WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             12              337
[1] 2 2
[1] FALSE

Clustering(357) Variable = ZBTB5 MUTATION ANALYSIS
D357V1, survival
                 sevent
clus2               0   1
  ZBTB5 MUTATED     2   1
  ZBTB5 WILD-TYPE 313 140
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              3             453 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              1             140 
$`ZBTB5 MUTATED`
TCGA-55-8085 TCGA-78-7155 TCGA-93-8067 
       29.72        38.50         6.12 

$`ZBTB5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 
        6.48        17.65         6.15        19.82         0.16        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        9.76         4.18        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
           6.12            0.00 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
          38.50          223.96 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
          29.72           17.98 
[1] "6.1 - 38.5 (29.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1"  
D357V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZBTB5 MUTATED         0        1        2         0         0          0
  ZBTB5 WILD-TYPE       4      122      131        46        67         70
                 vv
clus              STAGE IIIB STAGE IV
  ZBTB5 MUTATED            0        0
  ZBTB5 WILD-TYPE         11       25
D357V3, multiclass
            clus
vv           ZBTB5 MUTATED ZBTB5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               2             131
  STAGE IIA              0              46
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZBTB5 MUTATED     1   2   0   0
  ZBTB5 WILD-TYPE 154 259  43  18
D357V4, multiclass
    clus
vv   ZBTB5 MUTATED ZBTB5 WILD-TYPE
  T1             1             154
  T2             2             259
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  ZBTB5 MUTATED     3   0     0
  ZBTB5 WILD-TYPE 304  89    72
D357V5, multiclass
       clus
vv      ZBTB5 MUTATED ZBTB5 WILD-TYPE
  N0                3             304
  N1                0              89
  N2+N3             0              72
[1] 3 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
  ZBTB5 MUTATED     2   0
  ZBTB5 WILD-TYPE 325  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      2    0
  ZBTB5 WILD-TYPE  325   23
   clus
vv  ZBTB5 MUTATED ZBTB5 WILD-TYPE
  0             2             325
  1             0              23
[1] 2 2
[1] FALSE
D357V7, binary
                 cls
clus                0   1
  ZBTB5 MUTATED     0   3
  ZBTB5 WILD-TYPE 259 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      0    3
  ZBTB5 WILD-TYPE  259  218
        clus
vv       ZBTB5 MUTATED ZBTB5 WILD-TYPE
  FEMALE             0             259
  MALE               3             218
[1] 2 2
[1] FALSE
D357V8, continuous
[1] "Remove cluster labels:" "ZBTB5 MUTATED"         
clus
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZBTB5 MUTATED                            0                                 0
  ZBTB5 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZBTB5 MUTATED                                                    2
  ZBTB5 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZBTB5 MUTATED                                            0
  ZBTB5 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZBTB5 MUTATED                                               0
  ZBTB5 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ZBTB5 MUTATED                                0
  ZBTB5 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ZBTB5 MUTATED                                    0
  ZBTB5 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZBTB5 MUTATED                              0                             1
  ZBTB5 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZBTB5 MUTATED                                               0
  ZBTB5 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ZBTB5 MUTATED                              0
  ZBTB5 WILD-TYPE                            9
D357V9, multiclass
                                                    clus
vv                                                   ZBTB5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ZBTB5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V10, binary
                 cls
clus                0   1
  ZBTB5 MUTATED     0   3
  ZBTB5 WILD-TYPE  20 457
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      0    3
  ZBTB5 WILD-TYPE   20  457
     clus
vv    ZBTB5 MUTATED ZBTB5 WILD-TYPE
  NO              0              20
  YES             3             457
[1] 2 2
[1] FALSE
D357V11, continuous
[1] "Remove cluster labels:" "ZBTB5 MUTATED"         
clus
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              2             331 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4396 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4397      TCGA-05-4398      TCGA-05-4405      TCGA-05-4410 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4415      TCGA-05-4417      TCGA-05-4418      TCGA-05-4420 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4422      TCGA-05-4424      TCGA-05-4425      TCGA-05-4426 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4430      TCGA-05-4432      TCGA-05-4433 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4434      TCGA-05-5420      TCGA-05-5423      TCGA-05-5425 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-5428      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-38-4625      TCGA-38-4626      TCGA-38-4629      TCGA-38-4631 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-38-4632      TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-3396      TCGA-44-3398      TCGA-44-3918 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-4112      TCGA-44-5643      TCGA-44-5644      TCGA-44-5645 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6145      TCGA-44-6146      TCGA-44-6148 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-6774      TCGA-44-6775      TCGA-44-6776      TCGA-44-6777 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-6778      TCGA-44-6779      TCGA-44-7659      TCGA-44-7660 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-7661      TCGA-44-7662      TCGA-44-7667      TCGA-44-7669 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-7670      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4490      TCGA-49-4494 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4507      TCGA-49-4510 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-49-4514      TCGA-49-6742      TCGA-49-6743      TCGA-49-6744 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-49-6745      TCGA-49-6761      TCGA-49-6767      TCGA-50-5051 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-50-5072      TCGA-50-5931      TCGA-50-5939      TCGA-50-5941 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-50-5942      TCGA-50-6590      TCGA-50-7109      TCGA-50-8457 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-50-8459      TCGA-53-7624      TCGA-53-7626      TCGA-53-7813 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-6543      TCGA-55-6971      TCGA-55-6983 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-6985      TCGA-55-7281      TCGA-55-7283      TCGA-55-7574 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7724      TCGA-55-7725      TCGA-55-7726      TCGA-55-7728 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7903      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-7994      TCGA-55-7995      TCGA-55-8089 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8203      TCGA-55-8205      TCGA-55-8208      TCGA-55-8299 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8301      TCGA-55-8302      TCGA-55-8507      TCGA-55-8511 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8514      TCGA-55-8614      TCGA-55-8615 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-A46O      TCGA-62-A46P 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A470      TCGA-62-A471 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1676      TCGA-64-1677      TCGA-64-1679 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-64-5774      TCGA-64-5775      TCGA-64-5778      TCGA-64-5779 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-64-5781      TCGA-64-5815      TCGA-69-7761      TCGA-69-7763 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-69-7764      TCGA-69-7973      TCGA-69-7974      TCGA-69-7978 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-69-7979      TCGA-69-7980      TCGA-69-8253      TCGA-69-8254 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-69-8255      TCGA-69-A59K      TCGA-73-4658      TCGA-73-4659 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-7498      TCGA-75-5122 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-75-5125      TCGA-75-5126      TCGA-75-6203      TCGA-75-6206 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-75-6207      TCGA-75-6211      TCGA-75-6214      TCGA-75-7027 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7145      TCGA-78-7146      TCGA-78-7147 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7148      TCGA-78-7149      TCGA-78-7150      TCGA-78-7152 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7153      TCGA-78-7154      TCGA-78-7156      TCGA-78-7158 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-80-5608      TCGA-80-5611      TCGA-83-5908      TCGA-86-6851 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7714      TCGA-86-7954 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8673      TCGA-86-8674      TCGA-91-6829 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-91-6830      TCGA-91-6835      TCGA-91-6836      TCGA-91-6840 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-91-6849      TCGA-91-7771      TCGA-91-8499      TCGA-91-A4BC 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-95-7039      TCGA-95-7043      TCGA-95-7562      TCGA-95-7944 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-95-7947      TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547      TCGA-97-7552 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7937      TCGA-97-7938 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-7941      TCGA-97-8171      TCGA-97-8172      TCGA-97-8174 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-8176      TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-A4M1      TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025      TCGA-99-8028 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-99-8032      TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-L4-A4E5      TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY      TCGA-MP-A4T2 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7      TCGA-MP-A4T8 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TD 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YF      TCGA-NJ-A4YG 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ      TCGA-NJ-A55A 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
D357V12, continuous
[1] "Remove cluster labels:" "ZBTB5 MUTATED"         
clus
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              2             255 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6642 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-6712      TCGA-55-6971      TCGA-55-7227      TCGA-55-7283 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7907 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-8089 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8506      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8615      TCGA-55-8620      TCGA-55-8621 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-55-A491      TCGA-55-A492      TCGA-55-A493      TCGA-55-A494 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-62-8398      TCGA-64-1677      TCGA-64-1681      TCGA-64-5774 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-69-7761      TCGA-69-7763      TCGA-69-7764      TCGA-69-7765 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7979      TCGA-69-8253      TCGA-69-8255 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4675      TCGA-73-4676 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-73-7498      TCGA-75-6214      TCGA-75-7025      TCGA-75-7027 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-75-7031      TCGA-78-7145      TCGA-78-7146      TCGA-78-7147 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7148      TCGA-78-7149      TCGA-78-7150      TCGA-78-7152 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7153      TCGA-78-7154      TCGA-78-7156      TCGA-78-7158 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-80-5608      TCGA-83-5908      TCGA-86-6851      TCGA-86-7711 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-8054      TCGA-86-8055 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8281 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8673 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-91-6829      TCGA-91-6830 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043      TCGA-95-7562 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-95-7567      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP      TCGA-97-7546 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7941      TCGA-97-8171 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-8172      TCGA-97-8174      TCGA-97-8176      TCGA-97-8179 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7      TCGA-99-7458 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-99-8025      TCGA-99-8028      TCGA-99-8032      TCGA-J2-8194 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4T2 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8      TCGA-MP-A4T9 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE      TCGA-MP-A4TF 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" "ZBTB5 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  ZBTB5 MUTATED     2   0   0   1
  ZBTB5 WILD-TYPE 308  11   4  24
D357V13, multiclass
    clus
vv   ZBTB5 MUTATED ZBTB5 WILD-TYPE
  R0             2             308
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB5 MUTATED                                  0     1
  ZBTB5 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZBTB5 MUTATED                           0     2
  ZBTB5 WILD-TYPE                        29   375
D357V14, multiclass
                                  clus
vv                                 ZBTB5 MUTATED ZBTB5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        2             375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V15, binary
                 cls
clus                0   1
  ZBTB5 MUTATED     0   2
  ZBTB5 WILD-TYPE   6 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      0    2
  ZBTB5 WILD-TYPE    6  347
                        clus
vv                       ZBTB5 MUTATED ZBTB5 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2             347
[1] 2 2
[1] FALSE

Clustering(358) Variable = FANCM MUTATION ANALYSIS
D358V1, survival
                 sevent
clus2               0   1
  FANCM MUTATED    19  10
  FANCM WILD-TYPE 296 131
  FANCM MUTATED FANCM WILD-TYPE 
             29             427 
  FANCM MUTATED FANCM WILD-TYPE 
             10             131 
$`FANCM MUTATED`
TCGA-05-4382 TCGA-05-5425 TCGA-35-5375 TCGA-44-3918 TCGA-44-6774 TCGA-44-7662 
       19.96        29.00         8.68        34.06        21.63         7.17 
TCGA-49-4487 TCGA-50-5049 TCGA-50-6591 TCGA-53-7624 TCGA-55-6968 TCGA-55-6985 
       28.11        70.55         3.91        34.29        42.51        40.54 
TCGA-55-7994 TCGA-55-8302 TCGA-55-A491 TCGA-55-A4DF TCGA-62-A46O TCGA-67-3771 
       19.82         0.76        20.58        20.19        47.80        20.05 
TCGA-78-7220 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-91-6829 TCGA-91-7771 
       26.53        24.33         0.79        16.08        41.36        16.18 
TCGA-91-A4BC TCGA-95-7039 TCGA-97-8174 TCGA-97-8176 TCGA-97-A4M5 
        1.45         1.12         5.39        15.39        20.84 

$`FANCM WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
       23.77        10.78         9.93        27.78        23.15        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       12.03        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 
       11.08        11.54        13.64        13.45        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       17.16        11.64        22.26        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        22.55        42.35        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       48.62         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
        2.20        45.34        32.71        60.03        24.99       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40         1.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        29.98        26.30        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        4.57        15.75        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        5.95         0.59         0.72        18.67        17.92        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       19.76        20.52        17.75        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  FANCM MUTATED FANCM WILD-TYPE 
           0.76            0.00 
  FANCM MUTATED FANCM WILD-TYPE 
          70.55          223.96 
  FANCM MUTATED FANCM WILD-TYPE 
          20.19           17.72 
[1] "0.8 - 70.5 (20.2)"  "0.0 - 224.0 (17.7)"
[1] "hr=" "1.2"
D358V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FANCM MUTATED         0        8        8         3         5          4
  FANCM WILD-TYPE       4      115      125        43        62         66
                 vv
clus              STAGE IIIB STAGE IV
  FANCM MUTATED            0        3
  FANCM WILD-TYPE         11       22
D358V3, multiclass
            clus
vv           FANCM MUTATED FANCM WILD-TYPE
  STAGE I                0               4
  STAGE IA               8             115
  STAGE IB               8             125
  STAGE IIA              3              43
  STAGE IIB              5              62
  STAGE IIIA             4              66
  STAGE IIIB             0              11
  STAGE IV               3              22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FANCM MUTATED    10  17   4   0
  FANCM WILD-TYPE 145 244  39  18
D358V4, multiclass
    clus
vv   FANCM MUTATED FANCM WILD-TYPE
  T1            10             145
  T2            17             244
  T3             4              39
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  FANCM MUTATED    24   4     3
  FANCM WILD-TYPE 283  85    69
D358V5, multiclass
       clus
vv      FANCM MUTATED FANCM WILD-TYPE
  N0               24             283
  N1                4              85
  N2+N3             3              69
[1] 3 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
  FANCM MUTATED    18   3
  FANCM WILD-TYPE 309  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCM MUTATED     18    3
  FANCM WILD-TYPE  309   20
   clus
vv  FANCM MUTATED FANCM WILD-TYPE
  0            18             309
  1             3              20
[1] 2 2
[1] FALSE
D358V7, binary
                 cls
clus                0   1
  FANCM MUTATED    13  18
  FANCM WILD-TYPE 246 203
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCM MUTATED     13   18
  FANCM WILD-TYPE  246  203
        clus
vv       FANCM MUTATED FANCM WILD-TYPE
  FEMALE            13             246
  MALE              18             203
[1] 2 2
[1] FALSE
D358V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FANCM MUTATED                            1                                 5
  FANCM WILD-TYPE                         17                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FANCM MUTATED                                                   21
  FANCM WILD-TYPE                                                273
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FANCM MUTATED                                            0
  FANCM WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FANCM MUTATED                                               2
  FANCM WILD-TYPE                                            17
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FANCM MUTATED                                0
  FANCM WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FANCM MUTATED                                    0
  FANCM WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FANCM MUTATED                              0                             2
  FANCM WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FANCM MUTATED                                               0
  FANCM WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FANCM MUTATED                              0
  FANCM WILD-TYPE                            9
D358V9, multiclass
                                                    clus
vv                                                   FANCM MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            21
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  2
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FANCM WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             273
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   17
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V10, binary
                 cls
clus                0   1
  FANCM MUTATED     3  28
  FANCM WILD-TYPE  17 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCM MUTATED      3   28
  FANCM WILD-TYPE   17  432
     clus
vv    FANCM MUTATED FANCM WILD-TYPE
  NO              3              17
  YES            28             432
[1] 2 2
[1] FALSE
D358V11, continuous
D358V12, continuous
                 vv
clus               R0  R1  R2  RX
  FANCM MUTATED    21   0   0   0
  FANCM WILD-TYPE 289  11   4  25
D358V13, multiclass
    clus
vv   FANCM MUTATED FANCM WILD-TYPE
  R0            21             289
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FANCM MUTATED                                  0     0
  FANCM WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FANCM MUTATED                           1    26
  FANCM WILD-TYPE                        28   351
D358V14, multiclass
                                  clus
vv                                 FANCM MUTATED FANCM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       26             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V15, binary
                 cls
clus                0   1
  FANCM MUTATED     1  23
  FANCM WILD-TYPE   5 326
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCM MUTATED      1   23
  FANCM WILD-TYPE    5  326
                        clus
vv                       FANCM MUTATED FANCM WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            23             326
[1] 2 2
[1] FALSE

Clustering(359) Variable = MYOF MUTATION ANALYSIS
D359V1, survival
                sevent
clus2              0   1
  MYOF MUTATED    11   5
  MYOF WILD-TYPE 304 136
  MYOF MUTATED MYOF WILD-TYPE 
            16            440 
  MYOF MUTATED MYOF WILD-TYPE 
             5            136 
$`MYOF MUTATED`
TCGA-05-4390 TCGA-05-4422 TCGA-44-5644 TCGA-44-6774 TCGA-44-7662 TCGA-50-7109 
       37.02        12.00        28.37        21.63         7.17        10.13 
TCGA-53-7626 TCGA-55-5899 TCGA-55-6983 TCGA-55-8085 TCGA-55-8092 TCGA-55-8299 
       30.54         2.86        60.03        29.72         5.06        15.42 
TCGA-55-A494 TCGA-62-A470 TCGA-97-7554 TCGA-MN-A4N1 
       15.81        39.25        25.48        27.19 

$`MYOF WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        29.98        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       41.69         0.72        25.61         7.59        27.25        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
       13.94         9.21        23.05        48.62         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        15.19         3.29        19.66        19.73 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 
       56.71        54.35        67.96        72.30        13.61        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       19.89        31.69        64.60        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81         0.20        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  MYOF MUTATED MYOF WILD-TYPE 
          2.86           0.00 
  MYOF MUTATED MYOF WILD-TYPE 
         60.03         223.96 
  MYOF MUTATED MYOF WILD-TYPE 
        23.555         17.950 
[1] "2.9 - 60.0 (23.6)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D359V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MYOF MUTATED         0        4        6         2         2          2
  MYOF WILD-TYPE       4      119      127        44        65         68
                vv
clus             STAGE IIIB STAGE IV
  MYOF MUTATED            0        0
  MYOF WILD-TYPE         11       25
D359V3, multiclass
            clus
vv           MYOF MUTATED MYOF WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              6            127
  STAGE IIA             2             44
  STAGE IIB             2             65
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYOF MUTATED     6   9   1   0
  MYOF WILD-TYPE 149 252  42  18
D359V4, multiclass
    clus
vv   MYOF MUTATED MYOF WILD-TYPE
  T1            6            149
  T2            9            252
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  MYOF MUTATED    10   4     2
  MYOF WILD-TYPE 297  85    70
D359V5, multiclass
       clus
vv      MYOF MUTATED MYOF WILD-TYPE
  N0              10            297
  N1               4             85
  N2+N3            2             70
[1] 3 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
  MYOF MUTATED    11   0
  MYOF WILD-TYPE 316  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOF MUTATED     11    0
  MYOF WILD-TYPE  316   23
   clus
vv  MYOF MUTATED MYOF WILD-TYPE
  0           11            316
  1            0             23
[1] 2 2
[1] FALSE
D359V7, binary
                cls
clus               0   1
  MYOF MUTATED     7   9
  MYOF WILD-TYPE 252 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOF MUTATED      7    9
  MYOF WILD-TYPE  252  212
        clus
vv       MYOF MUTATED MYOF WILD-TYPE
  FEMALE            7            252
  MALE              9            212
[1] 2 2
[1] FALSE
D359V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MYOF MUTATED                            1                                 2
  MYOF WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MYOF MUTATED                                                   10
  MYOF WILD-TYPE                                                284
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MYOF MUTATED                                            0
  MYOF WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MYOF MUTATED                                               0
  MYOF WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MYOF MUTATED                                0
  MYOF WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MYOF MUTATED                                    0
  MYOF WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MYOF MUTATED                              0                             2
  MYOF WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MYOF MUTATED                                               0
  MYOF WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MYOF MUTATED                              1
  MYOF WILD-TYPE                            8
D359V9, multiclass
                                                    clus
vv                                                   MYOF MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   MYOF WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V10, binary
                cls
clus               0   1
  MYOF MUTATED     1  15
  MYOF WILD-TYPE  19 445
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOF MUTATED      1   15
  MYOF WILD-TYPE   19  445
     clus
vv    MYOF MUTATED MYOF WILD-TYPE
  NO             1             19
  YES           15            445
[1] 2 2
[1] FALSE
D359V11, continuous
D359V12, continuous
                vv
clus              R0  R1  R2  RX
  MYOF MUTATED    12   0   0   0
  MYOF WILD-TYPE 298  11   4  25
D359V13, multiclass
    clus
vv   MYOF MUTATED MYOF WILD-TYPE
  R0           12            298
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYOF MUTATED                                  0     0
  MYOF WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYOF MUTATED                           1    13
  MYOF WILD-TYPE                        28   364
D359V14, multiclass
                                  clus
vv                                 MYOF MUTATED MYOF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      13            364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V15, binary
                cls
clus               0   1
  MYOF MUTATED     0  14
  MYOF WILD-TYPE   6 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOF MUTATED      0   14
  MYOF WILD-TYPE    6  335
                        clus
vv                       MYOF MUTATED MYOF WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           14            335
[1] 2 2
[1] FALSE

Clustering(360) Variable = HNRNPA3 MUTATION ANALYSIS
D360V1, survival
                   sevent
clus2                 0   1
  HNRNPA3 MUTATED     6   1
  HNRNPA3 WILD-TYPE 309 140
  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
                7               449 
  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
                1               140 
$`HNRNPA3 MUTATED`
TCGA-05-4424 TCGA-44-A4SS TCGA-55-7911 TCGA-55-8096 TCGA-69-7979 TCGA-95-7039 
       30.02        13.64        17.65        23.64         2.93         1.12 
TCGA-NJ-A4YQ 
       29.13 

$`HNRNPA3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 
        1.78         1.45        18.64         0.53         6.48         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06         0.13        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.30        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64         0.26         0.43        19.82        59.11 

  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
             1.12              0.00 
  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
            30.02            223.96 
  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
            17.65             18.08 
[1] "1.1 - 30.0 (17.6)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.4"
D360V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HNRNPA3 MUTATED         0        3        2         0         2          0
  HNRNPA3 WILD-TYPE       4      120      131        46        65         70
                   vv
clus                STAGE IIIB STAGE IV
  HNRNPA3 MUTATED            0        0
  HNRNPA3 WILD-TYPE         11       25
D360V3, multiclass
            clus
vv           HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 3               120
  STAGE IB                 2               131
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HNRNPA3 MUTATED     3   2   2   0
  HNRNPA3 WILD-TYPE 152 259  41  18
D360V4, multiclass
    clus
vv   HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  T1               3               152
  T2               2               259
  T3               2                41
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  HNRNPA3 MUTATED     7   0     0
  HNRNPA3 WILD-TYPE 300  89    72
D360V5, multiclass
       clus
vv      HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  N0                  7               300
  N1                  0                89
  N2+N3               0                72
[1] 3 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
  HNRNPA3 MUTATED     3   0
  HNRNPA3 WILD-TYPE 324  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPA3 MUTATED      3    0
  HNRNPA3 WILD-TYPE  324   23
   clus
vv  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  0               3               324
  1               0                23
[1] 2 2
[1] FALSE
D360V7, binary
                   cls
clus                  0   1
  HNRNPA3 MUTATED     5   2
  HNRNPA3 WILD-TYPE 254 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPA3 MUTATED      5    2
  HNRNPA3 WILD-TYPE  254  219
        clus
vv       HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  FEMALE               5               254
  MALE                 2               219
[1] 2 2
[1] FALSE
D360V8, continuous
[1] "Remove cluster labels:" "HNRNPA3 MUTATED"       
clus
  HNRNPA3 MUTATED HNRNPA3 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8205        TCGA-55-8208 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8511        TCGA-55-8512 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5778 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-8254        TCGA-71-6725        TCGA-71-8520 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-73-4676        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-7955        TCGA-86-8055 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" "HNRNPA3 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  HNRNPA3 MUTATED                            1
  HNRNPA3 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  HNRNPA3 MUTATED                                   2
  HNRNPA3 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HNRNPA3 MUTATED                                                    4
  HNRNPA3 WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HNRNPA3 MUTATED                                            0
  HNRNPA3 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HNRNPA3 MUTATED                                               0
  HNRNPA3 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  HNRNPA3 MUTATED                                0
  HNRNPA3 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  HNRNPA3 MUTATED                                    0
  HNRNPA3 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HNRNPA3 MUTATED                              0                             0
  HNRNPA3 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HNRNPA3 MUTATED                                               0
  HNRNPA3 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  HNRNPA3 MUTATED                              0
  HNRNPA3 WILD-TYPE                            9
D360V9, multiclass
                                                    clus
vv                                                   HNRNPA3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   HNRNPA3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V10, binary
                   cls
clus                  0   1
  HNRNPA3 MUTATED     0   7
  HNRNPA3 WILD-TYPE  20 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPA3 MUTATED      0    7
  HNRNPA3 WILD-TYPE   20  453
     clus
vv    HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  NO                0                20
  YES               7               453
[1] 2 2
[1] FALSE
D360V11, continuous
D360V12, continuous
                   vv
clus                 R0  R1  R2  RX
  HNRNPA3 MUTATED     1   1   0   1
  HNRNPA3 WILD-TYPE 309  10   4  24
D360V13, multiclass
    clus
vv   HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  R0               1               309
  R1               1                10
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPA3 MUTATED                                  0     0
  HNRNPA3 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HNRNPA3 MUTATED                           0     6
  HNRNPA3 WILD-TYPE                        29   371
D360V14, multiclass
                                  clus
vv                                 HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V15, binary
                   cls
clus                  0   1
  HNRNPA3 MUTATED     0   6
  HNRNPA3 WILD-TYPE   6 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPA3 MUTATED      0    6
  HNRNPA3 WILD-TYPE    6  343
                        clus
vv                       HNRNPA3 MUTATED HNRNPA3 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               6               343
[1] 2 2
[1] FALSE

Clustering(361) Variable = LRRFIP2 MUTATION ANALYSIS
D361V1, survival
                   sevent
clus2                 0   1
  LRRFIP2 MUTATED     4   3
  LRRFIP2 WILD-TYPE 311 138
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                7               449 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                3               138 
$`LRRFIP2 MUTATED`
TCGA-38-4625 TCGA-44-7669 TCGA-55-6970 TCGA-55-8089 TCGA-55-8511 TCGA-78-7155 
       97.74        18.87        15.25         3.29         0.30        38.50 
TCGA-91-6848 
        7.36 

$`LRRFIP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        42.51        40.73         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
        0.95         0.36         0.26         0.49        17.72         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
              0.3               0.0 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
            97.74            223.96 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
            15.25             18.08 
[1] "0.3 - 97.7 (15.2)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D361V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LRRFIP2 MUTATED         0        1        3         1         0          2
  LRRFIP2 WILD-TYPE       4      122      130        45        67         68
                   vv
clus                STAGE IIIB STAGE IV
  LRRFIP2 MUTATED            0        0
  LRRFIP2 WILD-TYPE         11       25
D361V3, multiclass
            clus
vv           LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 3               130
  STAGE IIA                1                45
  STAGE IIB                0                67
  STAGE IIIA               2                68
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of 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   5   0   0
  LRRFIP2 WILD-TYPE 153 256  43  18
D361V4, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  T1               2               153
  T2               5               256
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  LRRFIP2 MUTATED     4   1     2
  LRRFIP2 WILD-TYPE 303  88    70
D361V5, multiclass
       clus
vv      LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  N0                  4               303
  N1                  1                88
  N2+N3               2                70
[1] 3 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
  LRRFIP2 MUTATED     3   0
  LRRFIP2 WILD-TYPE 324  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      3    0
  LRRFIP2 WILD-TYPE  324   23
   clus
vv  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  0               3               324
  1               0                23
[1] 2 2
[1] FALSE
D361V7, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     3   4
  LRRFIP2 WILD-TYPE 256 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      3    4
  LRRFIP2 WILD-TYPE  256  217
        clus
vv       LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  FEMALE               3               256
  MALE                 4               217
[1] 2 2
[1] FALSE
D361V8, continuous
[1] "Remove cluster labels:" "LRRFIP2 MUTATED"       
clus
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                2                82 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8096        TCGA-55-8205        TCGA-55-8208 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8512        TCGA-55-8619 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A494 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-62-8394        TCGA-62-8395        TCGA-62-8397        TCGA-62-8398 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O        TCGA-62-A46P 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U        TCGA-62-A46V 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471        TCGA-62-A472 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1681        TCGA-64-5778        TCGA-69-7974 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-69-8254        TCGA-71-6725        TCGA-71-8520        TCGA-73-4659 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-73-4662        TCGA-73-4666        TCGA-73-4668        TCGA-73-4676 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-73-7498        TCGA-73-7499        TCGA-75-5122        TCGA-83-5908 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-86-7701        TCGA-86-7711        TCGA-86-7713        TCGA-86-7714 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-86-7954        TCGA-86-7955        TCGA-86-8055        TCGA-86-8056 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-86-8074        TCGA-86-8075        TCGA-86-8076        TCGA-86-8278 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8281        TCGA-86-8358        TCGA-86-8359 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-86-8668        TCGA-86-8669        TCGA-86-8671        TCGA-86-A4JF 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348        TCGA-93-8067 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458        TCGA-MN-A4N1 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5 
"LRRFIP2 WILD-TYPE" "LRRFIP2 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  LRRFIP2 MUTATED                            0
  LRRFIP2 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  LRRFIP2 MUTATED                                   0
  LRRFIP2 WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LRRFIP2 MUTATED                                                    6
  LRRFIP2 WILD-TYPE                                                288
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LRRFIP2 MUTATED                                            0
  LRRFIP2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LRRFIP2 MUTATED                                               0
  LRRFIP2 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  LRRFIP2 MUTATED                                0
  LRRFIP2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  LRRFIP2 MUTATED                                    0
  LRRFIP2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  LRRFIP2 MUTATED                              0                             1
  LRRFIP2 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LRRFIP2 MUTATED                                               0
  LRRFIP2 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  LRRFIP2 MUTATED                              0
  LRRFIP2 WILD-TYPE                            9
D361V9, multiclass
                                                    clus
vv                                                   LRRFIP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   LRRFIP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V10, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     0   7
  LRRFIP2 WILD-TYPE  20 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      0    7
  LRRFIP2 WILD-TYPE   20  453
     clus
vv    LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  NO                0                20
  YES               7               453
[1] 2 2
[1] FALSE
D361V11, continuous
D361V12, continuous
                   vv
clus                 R0  R1  R2  RX
  LRRFIP2 MUTATED     4   1   0   0
  LRRFIP2 WILD-TYPE 306  10   4  25
D361V13, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  R0               4               306
  R1               1                10
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRFIP2 MUTATED                                  0     0
  LRRFIP2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LRRFIP2 MUTATED                           1     6
  LRRFIP2 WILD-TYPE                        28   371
D361V14, multiclass
                                  clus
vv                                 LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          6               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V15, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     0   5
  LRRFIP2 WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      0    5
  LRRFIP2 WILD-TYPE    6  344
                        clus
vv                       LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(362) Variable = MYLK MUTATION ANALYSIS
D362V1, survival
                sevent
clus2              0   1
  MYLK MUTATED    14   5
  MYLK WILD-TYPE 301 136
  MYLK MUTATED MYLK WILD-TYPE 
            19            437 
  MYLK MUTATED MYLK WILD-TYPE 
             5            136 
$`MYLK MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4432 TCGA-38-4625 TCGA-44-2657 TCGA-44-8117 
       19.96         9.96        25.02        97.74        13.15        12.66 
TCGA-50-5049 TCGA-55-7995 TCGA-55-8506 TCGA-62-8399 TCGA-64-5775 TCGA-73-4666 
       70.55         0.16         0.36        88.64         2.04        26.30 
TCGA-78-7150 TCGA-91-6828 TCGA-91-6848 TCGA-93-7348 TCGA-MN-A4N1 TCGA-MP-A4T6 
       21.90        10.62         7.36         4.18        27.19        58.85 
TCGA-MP-A4TF 
       11.05 

$`MYLK WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        5.98         8.68       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       20.65        55.43        38.37        87.98        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58        35.93        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       17.62        13.64        26.47        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23        27.68         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        3.81         0.20        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23         2.43        10.09        29.46        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  MYLK MUTATED MYLK WILD-TYPE 
          0.16           0.00 
  MYLK MUTATED MYLK WILD-TYPE 
         97.74         223.96 
  MYLK MUTATED MYLK WILD-TYPE 
         13.15          18.08 
[1] "0.2 - 97.7 (13.2)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.5"
D362V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MYLK MUTATED         0        5        5         2         3          4
  MYLK WILD-TYPE       4      118      128        44        64         66
                vv
clus             STAGE IIIB STAGE IV
  MYLK MUTATED            1        1
  MYLK WILD-TYPE         10       24
D362V3, multiclass
            clus
vv           MYLK MUTATED MYLK WILD-TYPE
  STAGE I               0              4
  STAGE IA              5            118
  STAGE IB              5            128
  STAGE IIA             2             44
  STAGE IIB             3             64
  STAGE IIIA            4             66
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYLK MUTATED     6  12   1   2
  MYLK WILD-TYPE 149 249  42  16
D362V4, multiclass
    clus
vv   MYLK MUTATED MYLK WILD-TYPE
  T1            6            149
  T2           12            249
  T3            1             42
  T4            2             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"
                vv
clus              N0  N1 N2+N3
  MYLK MUTATED    13   4     3
  MYLK WILD-TYPE 294  85    69
D362V5, multiclass
       clus
vv      MYLK MUTATED MYLK WILD-TYPE
  N0              13            294
  N1               4             85
  N2+N3            3             69
[1] 3 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
  MYLK MUTATED    16   1
  MYLK WILD-TYPE 311  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYLK MUTATED     16    1
  MYLK WILD-TYPE  311   22
   clus
vv  MYLK MUTATED MYLK WILD-TYPE
  0           16            311
  1            1             22
[1] 2 2
[1] FALSE
D362V7, binary
                cls
clus               0   1
  MYLK MUTATED    10  11
  MYLK WILD-TYPE 249 210
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYLK MUTATED     10   11
  MYLK WILD-TYPE  249  210
        clus
vv       MYLK MUTATED MYLK WILD-TYPE
  FEMALE           10            249
  MALE             11            210
[1] 2 2
[1] FALSE
D362V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MYLK MUTATED                            0                                 3
  MYLK WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MYLK MUTATED                                                   17
  MYLK WILD-TYPE                                                277
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MYLK MUTATED                                            0
  MYLK WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MYLK MUTATED                                               0
  MYLK WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MYLK MUTATED                                0
  MYLK WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MYLK MUTATED                                    0
  MYLK WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MYLK MUTATED                              0                             1
  MYLK WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MYLK MUTATED                                               0
  MYLK WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MYLK MUTATED                              0
  MYLK WILD-TYPE                            9
D362V9, multiclass
                                                    clus
vv                                                   MYLK MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MYLK WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V10, binary
                cls
clus               0   1
  MYLK MUTATED     2  19
  MYLK WILD-TYPE  18 441
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYLK MUTATED      2   19
  MYLK WILD-TYPE   18  441
     clus
vv    MYLK MUTATED MYLK WILD-TYPE
  NO             2             18
  YES           19            441
[1] 2 2
[1] FALSE
D362V11, continuous
D362V12, continuous
                vv
clus              R0  R1  R2  RX
  MYLK MUTATED    18   0   0   0
  MYLK WILD-TYPE 292  11   4  25
D362V13, multiclass
    clus
vv   MYLK MUTATED MYLK WILD-TYPE
  R0           18            292
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYLK MUTATED                                  0     0
  MYLK WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYLK MUTATED                           1    15
  MYLK WILD-TYPE                        28   362
D362V14, multiclass
                                  clus
vv                                 MYLK MUTATED MYLK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      15            362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V15, binary
                cls
clus               0   1
  MYLK MUTATED     0  15
  MYLK WILD-TYPE   6 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYLK MUTATED      0   15
  MYLK WILD-TYPE    6  334
                        clus
vv                       MYLK MUTATED MYLK WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           15            334
[1] 2 2
[1] FALSE

Clustering(363) Variable = AMELX MUTATION ANALYSIS
D363V1, survival
                 sevent
clus2               0   1
  AMELX MUTATED     8   1
  AMELX WILD-TYPE 307 140
  AMELX MUTATED AMELX WILD-TYPE 
              9             447 
  AMELX MUTATED AMELX WILD-TYPE 
              1             140 
$`AMELX MUTATED`
TCGA-05-4405 TCGA-44-A479 TCGA-50-5049 TCGA-55-7910 TCGA-64-5781 TCGA-78-7158 
       20.05        15.98        70.55         6.48        51.25         5.88 
TCGA-86-6851 TCGA-86-8073 TCGA-NJ-A4YF 
        5.88        24.33        71.05 

$`AMELX WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       11.64        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         0.53        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 
       39.52        24.99        19.50        38.50        32.09        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  AMELX MUTATED AMELX WILD-TYPE 
           5.88            0.00 
  AMELX MUTATED AMELX WILD-TYPE 
          71.05          223.96 
  AMELX MUTATED AMELX WILD-TYPE 
          20.05           17.98 
[1] "5.9 - 71.0 (20.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "4"  
D363V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AMELX MUTATED         0        2        5         2         0          0
  AMELX WILD-TYPE       4      121      128        44        67         70
                 vv
clus              STAGE IIIB STAGE IV
  AMELX MUTATED            1        0
  AMELX WILD-TYPE         10       25
D363V3, multiclass
            clus
vv           AMELX MUTATED AMELX WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               5             128
  STAGE IIA              2              44
  STAGE IIB              0              67
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of 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     2   7   0   1
  AMELX WILD-TYPE 153 254  43  17
D363V4, multiclass
    clus
vv   AMELX MUTATED AMELX WILD-TYPE
  T1             2             153
  T2             7             254
  T3             0              43
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  AMELX MUTATED     8   1     1
  AMELX WILD-TYPE 299  88    71
D363V5, multiclass
       clus
vv      AMELX MUTATED AMELX WILD-TYPE
  N0                8             299
  N1                1              88
  N2+N3             1              71
[1] 3 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
  AMELX MUTATED     9   0
  AMELX WILD-TYPE 318  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      9    0
  AMELX WILD-TYPE  318   23
   clus
vv  AMELX MUTATED AMELX WILD-TYPE
  0             9             318
  1             0              23
[1] 2 2
[1] FALSE
D363V7, binary
                 cls
clus                0   1
  AMELX MUTATED     7   3
  AMELX WILD-TYPE 252 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      7    3
  AMELX WILD-TYPE  252  218
        clus
vv       AMELX MUTATED AMELX WILD-TYPE
  FEMALE             7             252
  MALE               3             218
[1] 2 2
[1] FALSE
D363V8, continuous
[1] "Remove cluster labels:" "AMELX MUTATED"         
clus
  AMELX MUTATED AMELX WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7914 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5778 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-83-5908      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-7955      TCGA-86-8055 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8281      TCGA-86-8358 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMELX MUTATED                            0                                 6
  AMELX WILD-TYPE                         18                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMELX MUTATED                                                    3
  AMELX WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMELX MUTATED                                            0
  AMELX WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMELX MUTATED                                               1
  AMELX WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  AMELX MUTATED                                0
  AMELX WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMELX MUTATED                                    0
  AMELX WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  AMELX MUTATED                              0                             0
  AMELX WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMELX MUTATED                                               0
  AMELX WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  AMELX MUTATED                              0
  AMELX WILD-TYPE                            9
D363V9, multiclass
                                                    clus
vv                                                   AMELX MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   AMELX WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V10, binary
                 cls
clus                0   1
  AMELX MUTATED     1   9
  AMELX WILD-TYPE  19 451
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      1    9
  AMELX WILD-TYPE   19  451
     clus
vv    AMELX MUTATED AMELX WILD-TYPE
  NO              1              19
  YES             9             451
[1] 2 2
[1] FALSE
D363V11, continuous
D363V12, continuous
                 vv
clus               R0  R1  R2  RX
  AMELX MUTATED     5   1   0   1
  AMELX WILD-TYPE 305  10   4  24
D363V13, multiclass
    clus
vv   AMELX MUTATED AMELX WILD-TYPE
  R0             5             305
  R1             1              10
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMELX MUTATED                                  0     0
  AMELX WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AMELX MUTATED                           3     5
  AMELX WILD-TYPE                        26   372
D363V14, multiclass
                                  clus
vv                                 AMELX MUTATED AMELX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              26
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V15, binary
                 cls
clus                0   1
  AMELX MUTATED     0   7
  AMELX WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      0    7
  AMELX WILD-TYPE    6  342
                        clus
vv                       AMELX MUTATED AMELX WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(364) Variable = TMEM145 MUTATION ANALYSIS
D364V1, survival
                   sevent
clus2                 0   1
  TMEM145 MUTATED     7   4
  TMEM145 WILD-TYPE 308 137
  TMEM145 MUTATED TMEM145 WILD-TYPE 
               11               445 
  TMEM145 MUTATED TMEM145 WILD-TYPE 
                4               137 
$`TMEM145 MUTATED`
TCGA-44-5644 TCGA-44-6777 TCGA-49-4488 TCGA-49-6767 TCGA-50-5049 TCGA-55-7281 
       28.37        32.45        28.57        22.26        70.55         0.59 
TCGA-55-7994 TCGA-55-A4DF TCGA-95-7947 TCGA-97-7938 TCGA-99-7458 
       19.82        20.19        15.68         0.59        24.56 

$`TMEM145 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 
       27.78        23.15        21.63        23.18        63.72        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.11        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         1.74         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  TMEM145 MUTATED TMEM145 WILD-TYPE 
             0.59              0.00 
  TMEM145 MUTATED TMEM145 WILD-TYPE 
            70.55            223.96 
  TMEM145 MUTATED TMEM145 WILD-TYPE 
            22.26             17.75 
[1] "0.6 - 70.5 (22.3)"  "0.0 - 224.0 (17.8)"
[1] "hr=" "1.2"
D364V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TMEM145 MUTATED         0        6        2         0         2          1
  TMEM145 WILD-TYPE       4      117      131        46        65         69
                   vv
clus                STAGE IIIB STAGE IV
  TMEM145 MUTATED            0        0
  TMEM145 WILD-TYPE         11       25
D364V3, multiclass
            clus
vv           TMEM145 MUTATED TMEM145 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 6               117
  STAGE IB                 2               131
  STAGE IIA                0                46
  STAGE IIB                2                65
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM145 MUTATED     5   3   2   1
  TMEM145 WILD-TYPE 150 258  41  17
D364V4, multiclass
    clus
vv   TMEM145 MUTATED TMEM145 WILD-TYPE
  T1               5               150
  T2               3               258
  T3               2                41
  T4               1                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"
                   vv
clus                 N0  N1 N2+N3
  TMEM145 MUTATED    10   0     0
  TMEM145 WILD-TYPE 297  89    72
D364V5, multiclass
       clus
vv      TMEM145 MUTATED TMEM145 WILD-TYPE
  N0                 10               297
  N1                  0                89
  N2+N3               0                72
[1] 3 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
  TMEM145 MUTATED     4   0
  TMEM145 WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM145 MUTATED      4    0
  TMEM145 WILD-TYPE  323   23
   clus
vv  TMEM145 MUTATED TMEM145 WILD-TYPE
  0               4               323
  1               0                23
[1] 2 2
[1] FALSE
D364V7, binary
                   cls
clus                  0   1
  TMEM145 MUTATED     7   4
  TMEM145 WILD-TYPE 252 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM145 MUTATED      7    4
  TMEM145 WILD-TYPE  252  217
        clus
vv       TMEM145 MUTATED TMEM145 WILD-TYPE
  FEMALE               7               252
  MALE                 4               217
[1] 2 2
[1] FALSE
D364V8, continuous
[1] "Remove cluster labels:" "TMEM145 MUTATED"       
clus
  TMEM145 MUTATED TMEM145 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8281 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-93-7348        TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" "TMEM145 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  TMEM145 MUTATED                            0
  TMEM145 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  TMEM145 MUTATED                                   1
  TMEM145 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TMEM145 MUTATED                                                    8
  TMEM145 WILD-TYPE                                                286
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TMEM145 MUTATED                                            0
  TMEM145 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TMEM145 MUTATED                                               2
  TMEM145 WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  TMEM145 MUTATED                                0
  TMEM145 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  TMEM145 MUTATED                                    0
  TMEM145 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TMEM145 MUTATED                              0                             0
  TMEM145 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TMEM145 MUTATED                                               0
  TMEM145 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  TMEM145 MUTATED                              0
  TMEM145 WILD-TYPE                            9
D364V9, multiclass
                                                    clus
vv                                                   TMEM145 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   TMEM145 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V10, binary
                   cls
clus                  0   1
  TMEM145 MUTATED     2   9
  TMEM145 WILD-TYPE  18 451
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM145 MUTATED      2    9
  TMEM145 WILD-TYPE   18  451
     clus
vv    TMEM145 MUTATED TMEM145 WILD-TYPE
  NO                2                18
  YES               9               451
[1] 2 2
[1] FALSE
D364V11, continuous
D364V12, continuous
                   vv
clus                 R0  R1  R2  RX
  TMEM145 MUTATED     8   0   0   0
  TMEM145 WILD-TYPE 302  11   4  25
D364V13, multiclass
    clus
vv   TMEM145 MUTATED TMEM145 WILD-TYPE
  R0               8               302
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM145 MUTATED                                  0     0
  TMEM145 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM145 MUTATED                           0    11
  TMEM145 WILD-TYPE                        29   366
D364V14, multiclass
                                  clus
vv                                 TMEM145 MUTATED TMEM145 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                         11               366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V15, binary
                   cls
clus                  0   1
  TMEM145 MUTATED     0   8
  TMEM145 WILD-TYPE   6 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM145 MUTATED      0    8
  TMEM145 WILD-TYPE    6  341
                        clus
vv                       TMEM145 MUTATED TMEM145 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               8               341
[1] 2 2
[1] FALSE

Clustering(365) Variable = GCDH MUTATION ANALYSIS
D365V1, survival
                sevent
clus2              0   1
  GCDH MUTATED     3   0
  GCDH WILD-TYPE 312 141
  GCDH MUTATED GCDH WILD-TYPE 
             3            453 
  GCDH MUTATED GCDH WILD-TYPE 
             0            141 
$`GCDH MUTATED`
TCGA-69-7979 TCGA-91-6848 TCGA-91-A4BC 
        2.93         7.36         1.45 

$`GCDH WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.18        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  GCDH MUTATED GCDH WILD-TYPE 
          1.45           0.00 
  GCDH MUTATED GCDH WILD-TYPE 
          7.36         223.96 
  GCDH MUTATED GCDH WILD-TYPE 
          2.93          18.12 
[1] "1.4 - 7.4 (2.9)"    "0.0 - 224.0 (18.1)"
[1] "hr="    "450000"
D365V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GCDH MUTATED         0        0        2         1         0          1
  GCDH WILD-TYPE       4      123      131        45        67         69
                vv
clus             STAGE IIIB STAGE IV
  GCDH MUTATED            0        0
  GCDH WILD-TYPE         11       25
D365V3, multiclass
            clus
vv           GCDH MUTATED GCDH WILD-TYPE
  STAGE I               0              4
  STAGE IA              0            123
  STAGE IB              2            131
  STAGE IIA             1             45
  STAGE IIB             0             67
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of 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   4   0   0
  GCDH WILD-TYPE 155 257  43  18
D365V4, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  T1            0            155
  T2            4            257
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  GCDH MUTATED     3   0     1
  GCDH WILD-TYPE 304  89    71
D365V5, multiclass
       clus
vv      GCDH MUTATED GCDH WILD-TYPE
  N0               3            304
  N1               0             89
  N2+N3            1             71
[1] 3 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
  GCDH MUTATED     1   0
  GCDH WILD-TYPE 326  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      1    0
  GCDH WILD-TYPE  326   23
   clus
vv  GCDH MUTATED GCDH WILD-TYPE
  0            1            326
  1            0             23
[1] 2 2
[1] FALSE
D365V7, binary
                cls
clus               0   1
  GCDH MUTATED     1   3
  GCDH WILD-TYPE 258 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      1    3
  GCDH WILD-TYPE  258  218
        clus
vv       GCDH MUTATED GCDH WILD-TYPE
  FEMALE            1            258
  MALE              3            218
[1] 2 2
[1] FALSE
D365V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GCDH MUTATED                            1                                 1
  GCDH WILD-TYPE                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GCDH MUTATED                                                    2
  GCDH WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GCDH MUTATED                                            0
  GCDH WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GCDH MUTATED                                               0
  GCDH WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  GCDH MUTATED                                0
  GCDH WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  GCDH MUTATED                                    0
  GCDH WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GCDH MUTATED                              0                             0
  GCDH WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GCDH MUTATED                                               0
  GCDH WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  GCDH MUTATED                              0
  GCDH WILD-TYPE                            9
D365V9, multiclass
                                                    clus
vv                                                   GCDH MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   GCDH WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V10, binary
                cls
clus               0   1
  GCDH MUTATED     0   4
  GCDH WILD-TYPE  20 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      0    4
  GCDH WILD-TYPE   20  456
     clus
vv    GCDH MUTATED GCDH WILD-TYPE
  NO             0             20
  YES            4            456
[1] 2 2
[1] FALSE
D365V11, continuous
D365V12, continuous
                vv
clus              R0  R1  R2  RX
  GCDH MUTATED     0   0   0   1
  GCDH WILD-TYPE 310  11   4  24
D365V13, multiclass
[1] "Remove cluster labels:" "GCDH MUTATED"          
clus
  GCDH MUTATED GCDH WILD-TYPE 
             1            349 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4415     TCGA-05-4417 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-4418     TCGA-05-4420     TCGA-05-4422     TCGA-05-4424 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-4425     TCGA-05-4426     TCGA-05-4427     TCGA-05-4430 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-4432     TCGA-05-4433     TCGA-05-4434     TCGA-05-5420 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-5423     TCGA-05-5425     TCGA-05-5428     TCGA-05-5429 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-05-5715     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-4627     TCGA-38-4628 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-38-4629     TCGA-38-4630     TCGA-38-4631     TCGA-38-4632 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F     TCGA-44-2657 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-44-2661     TCGA-44-2665     TCGA-44-3396     TCGA-44-3398 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-44-3918     TCGA-44-3919     TCGA-44-4112     TCGA-44-6144 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4486 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4488     TCGA-49-4494     TCGA-49-4501 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4507     TCGA-49-4510 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-49-4512     TCGA-49-4514     TCGA-49-6742     TCGA-49-6744 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-49-6761     TCGA-49-6767     TCGA-50-5051     TCGA-50-5055 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-50-5066     TCGA-50-5931     TCGA-50-5942     TCGA-50-5944 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-50-6593     TCGA-50-6597     TCGA-50-6673     TCGA-50-8460 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-1592 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-5899     TCGA-55-6642     TCGA-55-6970     TCGA-55-6971 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-6972     TCGA-55-6980     TCGA-55-6981     TCGA-55-6983 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-6985     TCGA-55-7281     TCGA-55-7284     TCGA-55-7570 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7727     TCGA-55-7728     TCGA-55-7815 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-7903     TCGA-55-7907     TCGA-55-7910     TCGA-55-7911 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-7914     TCGA-55-7994     TCGA-55-7995     TCGA-55-8085 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8087     TCGA-55-8089     TCGA-55-8090     TCGA-55-8091 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8097     TCGA-55-8203 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8204     TCGA-55-8205     TCGA-55-8206     TCGA-55-8207 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8505     TCGA-55-8506     TCGA-55-8507     TCGA-55-8508 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8510     TCGA-55-8511     TCGA-55-8512     TCGA-55-8513 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8614     TCGA-55-8615     TCGA-55-8616 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-55-A4DG     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1676     TCGA-64-1677     TCGA-64-1679 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5774     TCGA-64-5775     TCGA-64-5778 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-64-5779     TCGA-64-5781     TCGA-64-5815     TCGA-67-3771 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-67-3773     TCGA-67-4679     TCGA-67-6215     TCGA-67-6216 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-67-6217     TCGA-71-6725     TCGA-71-8520     TCGA-73-4658 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-4677 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-75-5125 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-75-5126     TCGA-75-5146     TCGA-75-5147     TCGA-75-6203 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-75-6205     TCGA-75-6206     TCGA-75-6207     TCGA-75-6211 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-75-6212     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-75-7030     TCGA-75-7031     TCGA-78-7143     TCGA-78-7145 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7540 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-80-5608     TCGA-80-5611     TCGA-83-5908     TCGA-86-6562 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-7953     TCGA-86-7954     TCGA-86-7955     TCGA-86-8054 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8073     TCGA-86-8074 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-8075     TCGA-86-8076     TCGA-86-8278     TCGA-86-8279 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-8280     TCGA-86-8358     TCGA-86-8359     TCGA-86-8585 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-8672 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-8673     TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6828     TCGA-91-6829     TCGA-91-6835 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-91-6840     TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-93-A4JQ     TCGA-95-7562     TCGA-95-7944     TCGA-95-7947 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-95-7948     TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7554     TCGA-97-7938     TCGA-97-7941 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-97-8176     TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-99-8033 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-L4-A4E6     TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-MP-A4SY     TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-MP-A4TC     TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-NJ-A4YQ 
"GCDH WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GCDH MUTATED                                  0     0
  GCDH WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GCDH MUTATED                           0     3
  GCDH WILD-TYPE                        29   374
D365V14, multiclass
                                  clus
vv                                 GCDH MUTATED GCDH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       3            374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V15, binary
                cls
clus               0   1
  GCDH MUTATED     0   3
  GCDH WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      0    3
  GCDH WILD-TYPE    6  346
                        clus
vv                       GCDH MUTATED GCDH WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(366) Variable = CACNA2D1 MUTATION ANALYSIS
D366V1, survival
                    sevent
clus2                  0   1
  CACNA2D1 MUTATED    28  12
  CACNA2D1 WILD-TYPE 287 129
  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
                40                416 
  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
                12                129 
$`CACNA2D1 MUTATED`
TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-7662 TCGA-49-4505 TCGA-49-6743 
       38.24        34.06        26.56         7.17        14.07        12.13 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5941 TCGA-50-7109 TCGA-55-1592 TCGA-55-5899 
       71.47        70.55        18.64        10.13        23.05         2.86 
TCGA-55-7576 TCGA-55-7903 TCGA-55-7994 TCGA-55-7995 TCGA-55-8206 TCGA-55-8506 
        1.32        18.64        19.82         0.16         1.51         0.36 
TCGA-55-8511 TCGA-55-A4DF TCGA-55-A4DG TCGA-64-1676 TCGA-64-1679 TCGA-64-5781 
        0.30        20.19        19.99        56.81        55.43        51.25 
TCGA-64-5815 TCGA-69-7978 TCGA-78-7145 TCGA-78-7147 TCGA-78-7537 TCGA-86-6851 
       28.47         2.30        27.16        19.27        53.33         5.88 
TCGA-86-8585 TCGA-86-A456 TCGA-95-7039 TCGA-97-A4M0 TCGA-99-8032 TCGA-L4-A4E5 
        1.15        13.32         1.12        21.44         1.45        19.00 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TF TCGA-MP-A4TI 
       27.19         5.29        11.05        14.10 

$`CACNA2D1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
       24.36        42.77        37.15         6.25        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       14.60        19.46        12.03        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5051 
       29.26        17.16        11.64        22.26        20.52        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       40.60        78.67        21.47         8.45        15.12        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21        41.69         0.72        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 
       27.25        34.29        30.54        13.94         9.21        48.62 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         3.12        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        6.15        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49        17.72         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
        0.92        15.81         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        38.37        87.98         2.04        42.90        28.41 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       39.09        23.51       163.10         5.69        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        8.48        88.14        26.53        31.20         8.02        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       15.65        15.85        23.05        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
       30.84        27.58         0.62        14.96        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85        36.76         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        35.47        16.44        14.30         3.81         0.20 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       86.04        58.85         5.49        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       10.09        29.46        14.66        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
              0.16               0.00 
  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
             71.47             223.96 
  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
             18.64              17.95 
[1] "0.2 - 71.5 (18.6)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D366V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CACNA2D1 MUTATED         1       15        8         4         7          4
  CACNA2D1 WILD-TYPE       3      108      125        42        60         66
                    vv
clus                 STAGE IIIB STAGE IV
  CACNA2D1 MUTATED            0        1
  CACNA2D1 WILD-TYPE         11       24
D366V3, multiclass
            clus
vv           CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 15                108
  STAGE IB                  8                125
  STAGE IIA                 4                 42
  STAGE IIB                 7                 60
  STAGE IIIA                4                 66
  STAGE IIIB                0                 11
  STAGE IV                  1                 24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CACNA2D1 MUTATED    16  20   3   1
  CACNA2D1 WILD-TYPE 139 241  40  17
D366V4, multiclass
    clus
vv   CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  T1               16                139
  T2               20                241
  T3                3                 40
  T4                1                 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"
                    vv
clus                  N0  N1 N2+N3
  CACNA2D1 MUTATED    26  10     4
  CACNA2D1 WILD-TYPE 281  79    68
D366V5, multiclass
       clus
vv      CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  N0                  26                281
  N1                  10                 79
  N2+N3                4                 68
[1] 3 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
  CACNA2D1 MUTATED    29   1
  CACNA2D1 WILD-TYPE 298  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D1 MUTATED     29    1
  CACNA2D1 WILD-TYPE  298   22
   clus
vv  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  0               29                298
  1                1                 22
[1] 2 2
[1] FALSE
D366V7, binary
                    cls
clus                   0   1
  CACNA2D1 MUTATED    20  20
  CACNA2D1 WILD-TYPE 239 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D1 MUTATED     20   20
  CACNA2D1 WILD-TYPE  239  201
        clus
vv       CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  FEMALE               20                239
  MALE                 20                201
[1] 2 2
[1] FALSE
D366V8, continuous
[1] "Remove cluster labels:" "CACNA2D1 MUTATED"      
clus
  CACNA2D1 MUTATED CACNA2D1 WILD-TYPE 
                 2                 82 
        TCGA-35-4122         TCGA-35-4123         TCGA-35-5375 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-53-A4EZ         TCGA-55-7283         TCGA-55-7573 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-55-7725         TCGA-55-7910         TCGA-55-7914 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-55-8089         TCGA-55-8096         TCGA-55-8205 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-55-8208         TCGA-55-8507         TCGA-55-8508 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-55-8512         TCGA-55-8619         TCGA-55-8620 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-55-A48Z         TCGA-55-A490         TCGA-55-A494 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-62-8394         TCGA-62-8395         TCGA-62-8397 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-62-8398         TCGA-62-8399         TCGA-62-8402 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-62-A46O         TCGA-62-A46P         TCGA-62-A46R 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-62-A46S         TCGA-62-A46U         TCGA-62-A46V 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-62-A46Y         TCGA-62-A470         TCGA-62-A471 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-62-A472         TCGA-64-1677         TCGA-64-1681 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-64-5778         TCGA-69-7974         TCGA-69-8254 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-71-6725         TCGA-71-8520         TCGA-73-4659 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-73-4662         TCGA-73-4666         TCGA-73-4668 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-73-4676         TCGA-73-7498         TCGA-73-7499 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-75-5122         TCGA-83-5908         TCGA-86-7701 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-86-7711         TCGA-86-7713         TCGA-86-7714 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-86-7954         TCGA-86-7955         TCGA-86-8055 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-86-8056         TCGA-86-8074         TCGA-86-8075 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-86-8076         TCGA-86-8278         TCGA-86-8279 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-86-8281         TCGA-86-8358         TCGA-86-8359 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-86-8668         TCGA-86-8669         TCGA-86-8671 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-86-A4JF         TCGA-86-A4P7         TCGA-91-6849 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-93-7348         TCGA-93-8067         TCGA-93-A4JN 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-93-A4JO         TCGA-99-7458         TCGA-MN-A4N4 
"CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" "CACNA2D1 WILD-TYPE" 
        TCGA-MN-A4N5 
"CACNA2D1 WILD-TYPE" 
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  CACNA2D1 MUTATED                            0
  CACNA2D1 WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  CACNA2D1 MUTATED                                   7
  CACNA2D1 WILD-TYPE                                95
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CACNA2D1 MUTATED                                                   30
  CACNA2D1 WILD-TYPE                                                264
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CACNA2D1 MUTATED                                            0
  CACNA2D1 WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CACNA2D1 MUTATED                                               0
  CACNA2D1 WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  CACNA2D1 MUTATED                                1
  CACNA2D1 WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  CACNA2D1 MUTATED                                    0
  CACNA2D1 WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CACNA2D1 MUTATED                              0                             1
  CACNA2D1 WILD-TYPE                            2                            21
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CACNA2D1 MUTATED                                               1
  CACNA2D1 WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  CACNA2D1 MUTATED                              0
  CACNA2D1 WILD-TYPE                            9
D366V9, multiclass
                                                    clus
vv                                                   CACNA2D1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   CACNA2D1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                264
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V10, binary
                    cls
clus                   0   1
  CACNA2D1 MUTATED     2  38
  CACNA2D1 WILD-TYPE  18 422
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D1 MUTATED      2   38
  CACNA2D1 WILD-TYPE   18  422
     clus
vv    CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  NO                 2                 18
  YES               38                422
[1] 2 2
[1] FALSE
D366V11, continuous
D366V12, continuous
                    vv
clus                  R0  R1  R2  RX
  CACNA2D1 MUTATED    29   1   0   0
  CACNA2D1 WILD-TYPE 281  10   4  25
D366V13, multiclass
    clus
vv   CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  R0               29                281
  R1                1                 10
  R2                0                  4
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA2D1 MUTATED                                  0     1
  CACNA2D1 WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CACNA2D1 MUTATED                           3    34
  CACNA2D1 WILD-TYPE                        26   343
D366V14, multiclass
                                  clus
vv                                 CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       3                 26
  WHITE                                          34                343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V15, binary
                    cls
clus                   0   1
  CACNA2D1 MUTATED     0  34
  CACNA2D1 WILD-TYPE   6 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CACNA2D1 MUTATED      0   34
  CACNA2D1 WILD-TYPE    6  315
                        clus
vv                       CACNA2D1 MUTATED CACNA2D1 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               34                315
[1] 2 2
[1] FALSE

Clustering(367) Variable = OR52E8 MUTATION ANALYSIS
D367V1, survival
                  sevent
clus2                0   1
  OR52E8 MUTATED    11   3
  OR52E8 WILD-TYPE 304 138
  OR52E8 MUTATED OR52E8 WILD-TYPE 
              14              442 
  OR52E8 MUTATED OR52E8 WILD-TYPE 
               3              138 
$`OR52E8 MUTATED`
TCGA-38-4631 TCGA-44-8119 TCGA-44-8120 TCGA-55-6975 TCGA-55-7574 TCGA-55-7994 
       11.64         3.25         8.55         3.88         3.12        19.82 
TCGA-55-8301 TCGA-55-A48X TCGA-55-A4DF TCGA-69-7978 TCGA-86-7713 TCGA-86-8056 
        1.45        22.65        20.19         2.30        13.87         4.57 
TCGA-97-8175 TCGA-99-8025 
       18.12        34.85 

$`OR52E8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 
       42.51        40.73        15.25         0.82        48.49         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92         5.39        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        24.56        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  OR52E8 MUTATED OR52E8 WILD-TYPE 
            1.45             0.00 
  OR52E8 MUTATED OR52E8 WILD-TYPE 
           34.85           223.96 
  OR52E8 MUTATED OR52E8 WILD-TYPE 
          10.095           18.410 
[1] "1.4 - 34.9 (10.1)"  "0.0 - 224.0 (18.4)"
[1] "hr=" "1.6"
D367V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  OR52E8 MUTATED         0        1        5         2         5          2
  OR52E8 WILD-TYPE       4      122      128        44        62         68
                  vv
clus               STAGE IIIB STAGE IV
  OR52E8 MUTATED            0        0
  OR52E8 WILD-TYPE         11       25
D367V3, multiclass
            clus
vv           OR52E8 MUTATED OR52E8 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                5              128
  STAGE IIA               2               44
  STAGE IIB               5               62
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR52E8 MUTATED     2   9   3   1
  OR52E8 WILD-TYPE 153 252  40  17
D367V4, multiclass
    clus
vv   OR52E8 MUTATED OR52E8 WILD-TYPE
  T1              2              153
  T2              9              252
  T3              3               40
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  OR52E8 MUTATED    10   4     1
  OR52E8 WILD-TYPE 297  85    71
D367V5, multiclass
       clus
vv      OR52E8 MUTATED OR52E8 WILD-TYPE
  N0                10              297
  N1                 4               85
  N2+N3              1               71
[1] 3 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
  OR52E8 MUTATED    11   0
  OR52E8 WILD-TYPE 316  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E8 MUTATED     11    0
  OR52E8 WILD-TYPE  316   23
   clus
vv  OR52E8 MUTATED OR52E8 WILD-TYPE
  0             11              316
  1              0               23
[1] 2 2
[1] FALSE
D367V7, binary
                  cls
clus                 0   1
  OR52E8 MUTATED     7   8
  OR52E8 WILD-TYPE 252 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E8 MUTATED      7    8
  OR52E8 WILD-TYPE  252  213
        clus
vv       OR52E8 MUTATED OR52E8 WILD-TYPE
  FEMALE              7              252
  MALE                8              213
[1] 2 2
[1] FALSE
D367V8, continuous
[1] "Remove cluster labels:" "OR52E8 MUTATED"        
clus
  OR52E8 MUTATED OR52E8 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"OR52E8 WILD-TYPE" "OR52E8 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  OR52E8 MUTATED                            0                                 3
  OR52E8 WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  OR52E8 MUTATED                                                   11
  OR52E8 WILD-TYPE                                                283
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  OR52E8 MUTATED                                            0
  OR52E8 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  OR52E8 MUTATED                                               0
  OR52E8 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  OR52E8 MUTATED                                0
  OR52E8 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  OR52E8 MUTATED                                    0
  OR52E8 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  OR52E8 MUTATED                              0                             0
  OR52E8 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  OR52E8 MUTATED                                               1
  OR52E8 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  OR52E8 MUTATED                              0
  OR52E8 WILD-TYPE                            9
D367V9, multiclass
                                                    clus
vv                                                   OR52E8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   OR52E8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V10, binary
                  cls
clus                 0   1
  OR52E8 MUTATED     1  14
  OR52E8 WILD-TYPE  19 446
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E8 MUTATED      1   14
  OR52E8 WILD-TYPE   19  446
     clus
vv    OR52E8 MUTATED OR52E8 WILD-TYPE
  NO               1               19
  YES             14              446
[1] 2 2
[1] FALSE
D367V11, continuous
D367V12, continuous
                  vv
clus                R0  R1  R2  RX
  OR52E8 MUTATED     9   1   0   0
  OR52E8 WILD-TYPE 301  10   4  25
D367V13, multiclass
    clus
vv   OR52E8 MUTATED OR52E8 WILD-TYPE
  R0              9              301
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR52E8 MUTATED                                  0     0
  OR52E8 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR52E8 MUTATED                           2    12
  OR52E8 WILD-TYPE                        27   365
D367V14, multiclass
                                  clus
vv                                 OR52E8 MUTATED OR52E8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        12              365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V15, binary
                  cls
clus                 0   1
  OR52E8 MUTATED     0  14
  OR52E8 WILD-TYPE   6 335
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E8 MUTATED      0   14
  OR52E8 WILD-TYPE    6  335
                        clus
vv                       OR52E8 MUTATED OR52E8 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             14              335
[1] 2 2
[1] FALSE

Clustering(368) Variable = ITGA2B MUTATION ANALYSIS
D368V1, survival
                  sevent
clus2                0   1
  ITGA2B MUTATED    10   2
  ITGA2B WILD-TYPE 305 139
  ITGA2B MUTATED ITGA2B WILD-TYPE 
              12              444 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               2              139 
$`ITGA2B MUTATED`
TCGA-44-3919 TCGA-44-5644 TCGA-44-8119 TCGA-50-5049 TCGA-55-7281 TCGA-55-8208 
        6.25        28.37         3.25        70.55         0.59        22.16 
TCGA-62-A46O TCGA-64-1679 TCGA-69-A59K TCGA-73-4670 TCGA-78-8662 TCGA-95-7039 
       47.80        55.43         7.04         4.31       110.50         1.12 

$`ITGA2B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
       24.36        42.77        37.15        38.24        34.06        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       18.87        29.00        17.59        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        71.47        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         1.74         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        20.65        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ITGA2B MUTATED ITGA2B WILD-TYPE 
            0.59             0.00 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
          110.50           223.96 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
           14.60            18.03 
[1] "0.6 - 110.5 (14.6)" "0.0 - 224.0 (18.0)"
[1] "hr=" "2.8"
D368V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ITGA2B MUTATED         0        4        3         0         3          1
  ITGA2B WILD-TYPE       4      119      130        46        64         69
                  vv
clus               STAGE IIIB STAGE IV
  ITGA2B MUTATED            0        1
  ITGA2B WILD-TYPE         11       24
D368V3, multiclass
            clus
vv           ITGA2B MUTATED ITGA2B WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                3              130
  STAGE IIA               0               46
  STAGE IIB               3               64
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ITGA2B MUTATED     4   5   3   0
  ITGA2B WILD-TYPE 151 256  40  18
D368V4, multiclass
    clus
vv   ITGA2B MUTATED ITGA2B WILD-TYPE
  T1              4              151
  T2              5              256
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ITGA2B MUTATED    11   0     1
  ITGA2B WILD-TYPE 296  89    71
D368V5, multiclass
       clus
vv      ITGA2B MUTATED ITGA2B WILD-TYPE
  N0                11              296
  N1                 0               89
  N2+N3              1               71
[1] 3 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
  ITGA2B MUTATED     9   1
  ITGA2B WILD-TYPE 318  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGA2B MUTATED      9    1
  ITGA2B WILD-TYPE  318   22
   clus
vv  ITGA2B MUTATED ITGA2B WILD-TYPE
  0              9              318
  1              1               22
[1] 2 2
[1] FALSE
D368V7, binary
                  cls
clus                 0   1
  ITGA2B MUTATED    10   2
  ITGA2B WILD-TYPE 249 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGA2B MUTATED     10    2
  ITGA2B WILD-TYPE  249  219
        clus
vv       ITGA2B MUTATED ITGA2B WILD-TYPE
  FEMALE             10              249
  MALE                2              219
[1] 2 2
[1] FALSE
D368V8, continuous
[1] "Remove cluster labels:" "ITGA2B MUTATED"        
clus
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46P 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5778       TCGA-69-7974 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4676 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ITGA2B MUTATED                            0                                 2
  ITGA2B WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ITGA2B MUTATED                                                   10
  ITGA2B WILD-TYPE                                                284
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ITGA2B MUTATED                                            0
  ITGA2B WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ITGA2B MUTATED                                               0
  ITGA2B WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ITGA2B MUTATED                                0
  ITGA2B WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ITGA2B MUTATED                                    0
  ITGA2B WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ITGA2B MUTATED                              0                             0
  ITGA2B WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ITGA2B MUTATED                                               0
  ITGA2B WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ITGA2B MUTATED                              0
  ITGA2B WILD-TYPE                            9
D368V9, multiclass
                                                    clus
vv                                                   ITGA2B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ITGA2B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V10, binary
                  cls
clus                 0   1
  ITGA2B MUTATED     1  11
  ITGA2B WILD-TYPE  19 449
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGA2B MUTATED      1   11
  ITGA2B WILD-TYPE   19  449
     clus
vv    ITGA2B MUTATED ITGA2B WILD-TYPE
  NO               1               19
  YES             11              449
[1] 2 2
[1] FALSE
D368V11, continuous
D368V12, continuous
                  vv
clus                R0  R1  R2  RX
  ITGA2B MUTATED     7   0   0   0
  ITGA2B WILD-TYPE 303  11   4  25
D368V13, multiclass
    clus
vv   ITGA2B MUTATED ITGA2B WILD-TYPE
  R0              7              303
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGA2B MUTATED                                  0     0
  ITGA2B WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ITGA2B MUTATED                           1    10
  ITGA2B WILD-TYPE                        28   367
D368V14, multiclass
                                  clus
vv                                 ITGA2B MUTATED ITGA2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V15, binary
                  cls
clus                 0   1
  ITGA2B MUTATED     0  10
  ITGA2B WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGA2B MUTATED      0   10
  ITGA2B WILD-TYPE    6  339
                        clus
vv                       ITGA2B MUTATED ITGA2B WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(369) Variable = GKN1 MUTATION ANALYSIS
D369V1, survival
                sevent
clus2              0   1
  GKN1 MUTATED     2   3
  GKN1 WILD-TYPE 313 138
  GKN1 MUTATED GKN1 WILD-TYPE 
             5            451 
  GKN1 MUTATED GKN1 WILD-TYPE 
             3            138 
$`GKN1 MUTATED`
TCGA-05-4418 TCGA-44-2657 TCGA-55-8208 TCGA-78-7220 TCGA-MP-A4TF 
        9.01        13.15        22.16        26.53        11.05 

$`GKN1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        46.98        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51         2.17        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      223.96         8.48        88.14        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  GKN1 MUTATED GKN1 WILD-TYPE 
          9.01           0.00 
  GKN1 MUTATED GKN1 WILD-TYPE 
         26.53         223.96 
  GKN1 MUTATED GKN1 WILD-TYPE 
         13.15          18.08 
[1] "9.0 - 26.5 (13.2)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "3.4"
D369V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GKN1 MUTATED         0        1        1         1         0          2
  GKN1 WILD-TYPE       4      122      132        45        67         68
                vv
clus             STAGE IIIB STAGE IV
  GKN1 MUTATED            0        0
  GKN1 WILD-TYPE         11       25
D369V3, multiclass
            clus
vv           GKN1 MUTATED GKN1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              1            132
  STAGE IIA             1             45
  STAGE IIB             0             67
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GKN1 MUTATED     1   3   1   0
  GKN1 WILD-TYPE 154 258  42  18
D369V4, multiclass
    clus
vv   GKN1 MUTATED GKN1 WILD-TYPE
  T1            1            154
  T2            3            258
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  GKN1 MUTATED     2   0     2
  GKN1 WILD-TYPE 305  89    70
D369V5, multiclass
       clus
vv      GKN1 MUTATED GKN1 WILD-TYPE
  N0               2            305
  N1               0             89
  N2+N3            2             70
[1] 3 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
  GKN1 MUTATED     5   0
  GKN1 WILD-TYPE 322  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      5    0
  GKN1 WILD-TYPE  322   23
   clus
vv  GKN1 MUTATED GKN1 WILD-TYPE
  0            5            322
  1            0             23
[1] 2 2
[1] FALSE
D369V7, binary
                cls
clus               0   1
  GKN1 MUTATED     4   1
  GKN1 WILD-TYPE 255 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      4    1
  GKN1 WILD-TYPE  255  220
        clus
vv       GKN1 MUTATED GKN1 WILD-TYPE
  FEMALE            4            255
  MALE              1            220
[1] 2 2
[1] FALSE
D369V8, continuous
[1] "Remove cluster labels:" "GKN1 MUTATED"          
clus
  GKN1 MUTATED GKN1 WILD-TYPE 
             1             83 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-53-A4EZ 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8511     TCGA-55-8512 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5778 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8281     TCGA-86-8358 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6849     TCGA-93-7348 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"GKN1 WILD-TYPE" "GKN1 WILD-TYPE" "GKN1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GKN1 MUTATED                            0                                 2
  GKN1 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GKN1 MUTATED                                                    3
  GKN1 WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GKN1 MUTATED                                            0
  GKN1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GKN1 MUTATED                                               0
  GKN1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  GKN1 MUTATED                                0
  GKN1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  GKN1 MUTATED                                    0
  GKN1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GKN1 MUTATED                              0                             0
  GKN1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GKN1 MUTATED                                               0
  GKN1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  GKN1 MUTATED                              0
  GKN1 WILD-TYPE                            9
D369V9, multiclass
                                                    clus
vv                                                   GKN1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   GKN1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V10, binary
                cls
clus               0   1
  GKN1 MUTATED     1   4
  GKN1 WILD-TYPE  19 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      1    4
  GKN1 WILD-TYPE   19  456
     clus
vv    GKN1 MUTATED GKN1 WILD-TYPE
  NO             1             19
  YES            4            456
[1] 2 2
[1] FALSE
D369V11, continuous
D369V12, continuous
                vv
clus              R0  R1  R2  RX
  GKN1 MUTATED     5   0   0   0
  GKN1 WILD-TYPE 305  11   4  25
D369V13, multiclass
    clus
vv   GKN1 MUTATED GKN1 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GKN1 MUTATED                                  0     0
  GKN1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GKN1 MUTATED                           0     4
  GKN1 WILD-TYPE                        29   373
D369V14, multiclass
                                  clus
vv                                 GKN1 MUTATED GKN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       4            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V15, binary
                cls
clus               0   1
  GKN1 MUTATED     0   3
  GKN1 WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      0    3
  GKN1 WILD-TYPE    6  346
                        clus
vv                       GKN1 MUTATED GKN1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(370) Variable = ADAM11 MUTATION ANALYSIS
D370V1, survival
                  sevent
clus2                0   1
  ADAM11 MUTATED    12   0
  ADAM11 WILD-TYPE 303 141
  ADAM11 MUTATED ADAM11 WILD-TYPE 
              12              444 
  ADAM11 MUTATED ADAM11 WILD-TYPE 
               0              141 
$`ADAM11 MUTATED`
TCGA-05-4382 TCGA-05-4424 TCGA-44-5643 TCGA-44-5644 TCGA-44-6147 TCGA-44-7671 
       19.96        30.02        33.30        28.37        27.78        17.59 
TCGA-50-5941 TCGA-55-7994 TCGA-55-8616 TCGA-69-A59K TCGA-86-8279 TCGA-MN-A4N4 
       18.64        19.82         1.58         7.04        15.85        38.63 

$`ADAM11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06         6.25        26.56        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       23.77        10.78         9.93        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
       12.03         7.17        36.07        18.87        29.00        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       15.12        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
        2.93        12.56        14.01        13.45         4.24         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       15.75        16.08        15.65        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ADAM11 MUTATED ADAM11 WILD-TYPE 
            1.58             0.00 
  ADAM11 MUTATED ADAM11 WILD-TYPE 
           38.63           223.96 
  ADAM11 MUTATED ADAM11 WILD-TYPE 
          19.890           17.835 
[1] "1.6 - 38.6 (19.9)"  "0.0 - 224.0 (17.8)"
[1] "hr="     "9300000"
D370V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADAM11 MUTATED         0        2        4         1         3          2
  ADAM11 WILD-TYPE       4      121      129        45        64         68
                  vv
clus               STAGE IIIB STAGE IV
  ADAM11 MUTATED            0        0
  ADAM11 WILD-TYPE         11       25
D370V3, multiclass
            clus
vv           ADAM11 MUTATED ADAM11 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                4              129
  STAGE IIA               1               45
  STAGE IIB               3               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM11 MUTATED     2   7   3   0
  ADAM11 WILD-TYPE 153 254  40  18
D370V4, multiclass
    clus
vv   ADAM11 MUTATED ADAM11 WILD-TYPE
  T1              2              153
  T2              7              254
  T3              3               40
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ADAM11 MUTATED     8   1     2
  ADAM11 WILD-TYPE 299  88    70
D370V5, multiclass
       clus
vv      ADAM11 MUTATED ADAM11 WILD-TYPE
  N0                 8              299
  N1                 1               88
  N2+N3              2               70
[1] 3 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
  ADAM11 MUTATED    10   0
  ADAM11 WILD-TYPE 317  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM11 MUTATED     10    0
  ADAM11 WILD-TYPE  317   23
   clus
vv  ADAM11 MUTATED ADAM11 WILD-TYPE
  0             10              317
  1              0               23
[1] 2 2
[1] FALSE
D370V7, binary
                  cls
clus                 0   1
  ADAM11 MUTATED     5   7
  ADAM11 WILD-TYPE 254 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM11 MUTATED      5    7
  ADAM11 WILD-TYPE  254  214
        clus
vv       ADAM11 MUTATED ADAM11 WILD-TYPE
  FEMALE              5              254
  MALE                7              214
[1] 2 2
[1] FALSE
D370V8, continuous
[1] "Remove cluster labels:" "ADAM11 MUTATED"        
clus
  ADAM11 MUTATED ADAM11 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4676       TCGA-73-7498       TCGA-73-7499 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-7701       TCGA-86-7711 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7954       TCGA-86-7955 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8074       TCGA-86-8075 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8281       TCGA-86-8358 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N5 
"ADAM11 WILD-TYPE" "ADAM11 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADAM11 MUTATED                            0                                 4
  ADAM11 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADAM11 MUTATED                                                    8
  ADAM11 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADAM11 MUTATED                                            0
  ADAM11 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADAM11 MUTATED                                               0
  ADAM11 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ADAM11 MUTATED                                0
  ADAM11 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ADAM11 MUTATED                                    0
  ADAM11 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADAM11 MUTATED                              0                             0
  ADAM11 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADAM11 MUTATED                                               0
  ADAM11 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ADAM11 MUTATED                              0
  ADAM11 WILD-TYPE                            9
D370V9, multiclass
                                                    clus
vv                                                   ADAM11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ADAM11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V10, binary
                  cls
clus                 0   1
  ADAM11 MUTATED     1  11
  ADAM11 WILD-TYPE  19 449
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM11 MUTATED      1   11
  ADAM11 WILD-TYPE   19  449
     clus
vv    ADAM11 MUTATED ADAM11 WILD-TYPE
  NO               1               19
  YES             11              449
[1] 2 2
[1] FALSE
D370V11, continuous
D370V12, continuous
                  vv
clus                R0  R1  R2  RX
  ADAM11 MUTATED     5   1   0   0
  ADAM11 WILD-TYPE 305  10   4  25
D370V13, multiclass
    clus
vv   ADAM11 MUTATED ADAM11 WILD-TYPE
  R0              5              305
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM11 MUTATED                                  0     0
  ADAM11 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM11 MUTATED                           3     7
  ADAM11 WILD-TYPE                        26   370
D370V14, multiclass
                                  clus
vv                                 ADAM11 MUTATED ADAM11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V15, binary
                  cls
clus                 0   1
  ADAM11 MUTATED     0   9
  ADAM11 WILD-TYPE   6 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM11 MUTATED      0    9
  ADAM11 WILD-TYPE    6  340
                        clus
vv                       ADAM11 MUTATED ADAM11 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              9              340
[1] 2 2
[1] FALSE

Clustering(371) Variable = FZD10 MUTATION ANALYSIS
D371V1, survival
                 sevent
clus2               0   1
  FZD10 MUTATED    21   7
  FZD10 WILD-TYPE 294 134
  FZD10 MUTATED FZD10 WILD-TYPE 
             28             428 
  FZD10 MUTATED FZD10 WILD-TYPE 
              7             134 
$`FZD10 MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-38-4626 TCGA-44-5644 TCGA-44-7670 TCGA-44-8117 
        9.96        20.05       120.79        28.37        29.00        12.66 
TCGA-44-A47A TCGA-49-4487 TCGA-55-7907 TCGA-55-7910 TCGA-55-8092 TCGA-55-8507 
       15.32        28.11         0.53         6.48         5.06         0.26 
TCGA-55-A493 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-69-7974 TCGA-78-7152 
        0.92        88.64        47.80        19.53         6.05        39.52 
TCGA-78-7155 TCGA-78-8662 TCGA-86-6851 TCGA-86-8279 TCGA-86-8671 TCGA-86-A4JF 
       38.50       110.50         5.88        15.85        27.58        17.62 
TCGA-95-7567 TCGA-99-7458 TCGA-99-8033 TCGA-NJ-A4YQ 
       18.67        24.56         5.59        29.13 

$`FZD10 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 
        0.00        24.03        47.05         8.02        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68        97.74        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       38.24        34.06         6.25        26.56        33.30        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       19.46        12.03         7.17        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
       23.64         3.25         8.55        15.98         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.78         1.45        18.64        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.36         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       19.59        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       42.38        14.60        49.25        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       32.68       214.62        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
        0.79        15.75        16.08        15.65        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 
       14.60         1.15        13.91        30.84         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        13.32        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        34.85        36.76         1.45 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  FZD10 MUTATED FZD10 WILD-TYPE 
           0.26            0.00 
  FZD10 MUTATED FZD10 WILD-TYPE 
         120.79          223.96 
  FZD10 MUTATED FZD10 WILD-TYPE 
          19.10           17.95 
[1] "0.3 - 120.8 (19.1)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D371V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FZD10 MUTATED         0        3       10         6         4          3
  FZD10 WILD-TYPE       4      120      123        40        63         67
                 vv
clus              STAGE IIIB STAGE IV
  FZD10 MUTATED            1        1
  FZD10 WILD-TYPE         10       24
D371V3, multiclass
            clus
vv           FZD10 MUTATED FZD10 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB              10             123
  STAGE IIA              6              40
  STAGE IIB              4              63
  STAGE IIIA             3              67
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FZD10 MUTATED     5  18   2   2
  FZD10 WILD-TYPE 150 243  41  16
D371V4, multiclass
    clus
vv   FZD10 MUTATED FZD10 WILD-TYPE
  T1             5             150
  T2            18             243
  T3             2              41
  T4             2              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"
                 vv
clus               N0  N1 N2+N3
  FZD10 MUTATED    18   7     2
  FZD10 WILD-TYPE 289  82    70
D371V5, multiclass
       clus
vv      FZD10 MUTATED FZD10 WILD-TYPE
  N0               18             289
  N1                7              82
  N2+N3             2              70
[1] 3 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
  FZD10 MUTATED    21   1
  FZD10 WILD-TYPE 306  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FZD10 MUTATED     21    1
  FZD10 WILD-TYPE  306   22
   clus
vv  FZD10 MUTATED FZD10 WILD-TYPE
  0            21             306
  1             1              22
[1] 2 2
[1] FALSE
D371V7, binary
                 cls
clus                0   1
  FZD10 MUTATED    17  11
  FZD10 WILD-TYPE 242 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FZD10 MUTATED     17   11
  FZD10 WILD-TYPE  242  210
        clus
vv       FZD10 MUTATED FZD10 WILD-TYPE
  FEMALE            17             242
  MALE              11             210
[1] 2 2
[1] FALSE
D371V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FZD10 MUTATED                            0                                 7
  FZD10 WILD-TYPE                         18                                95
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FZD10 MUTATED                                                   18
  FZD10 WILD-TYPE                                                276
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FZD10 MUTATED                                            0
  FZD10 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FZD10 MUTATED                                               1
  FZD10 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FZD10 MUTATED                                0
  FZD10 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FZD10 MUTATED                                    0
  FZD10 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FZD10 MUTATED                              0                             2
  FZD10 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FZD10 MUTATED                                               0
  FZD10 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FZD10 MUTATED                              0
  FZD10 WILD-TYPE                            9
D371V9, multiclass
                                                    clus
vv                                                   FZD10 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            18
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FZD10 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V10, binary
                 cls
clus                0   1
  FZD10 MUTATED     1  27
  FZD10 WILD-TYPE  19 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FZD10 MUTATED      1   27
  FZD10 WILD-TYPE   19  433
     clus
vv    FZD10 MUTATED FZD10 WILD-TYPE
  NO              1              19
  YES            27             433
[1] 2 2
[1] FALSE
D371V11, continuous
D371V12, continuous
                 vv
clus               R0  R1  R2  RX
  FZD10 MUTATED    21   0   0   1
  FZD10 WILD-TYPE 289  11   4  24
D371V13, multiclass
    clus
vv   FZD10 MUTATED FZD10 WILD-TYPE
  R0            21             289
  R1             0              11
  R2             0               4
  RX             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FZD10 MUTATED                                  0     0
  FZD10 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FZD10 MUTATED                           1    24
  FZD10 WILD-TYPE                        28   353
D371V14, multiclass
                                  clus
vv                                 FZD10 MUTATED FZD10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       24             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V15, binary
                 cls
clus                0   1
  FZD10 MUTATED     1  22
  FZD10 WILD-TYPE   5 327
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FZD10 MUTATED      1   22
  FZD10 WILD-TYPE    5  327
                        clus
vv                       FZD10 MUTATED FZD10 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            22             327
[1] 2 2
[1] FALSE

Clustering(372) Variable = TEC MUTATION ANALYSIS
D372V1, survival
               sevent
clus2             0   1
  TEC MUTATED     7   4
  TEC WILD-TYPE 308 137
  TEC MUTATED TEC WILD-TYPE 
           11           445 
  TEC MUTATED TEC WILD-TYPE 
            4           137 
$`TEC MUTATED`
TCGA-05-4432 TCGA-44-6775 TCGA-44-8119 TCGA-53-7624 TCGA-55-1595 TCGA-55-6979 
       25.02        23.18         3.25        34.29        48.62         7.79 
TCGA-55-7907 TCGA-55-8089 TCGA-78-7220 TCGA-86-7954 TCGA-91-6829 
        0.53         3.29        26.53        19.89        41.36 

$`TEC WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        21.63        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       18.87        29.00        17.59        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94         9.21        23.05 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 
       15.25         0.82        48.49         3.88         5.49         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 
        1.12         0.79         1.78         1.45        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
      104.19       223.96         8.48        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  TEC MUTATED TEC WILD-TYPE 
         0.53          0.00 
  TEC MUTATED TEC WILD-TYPE 
        48.62        223.96 
  TEC MUTATED TEC WILD-TYPE 
        23.18         17.92 
[1] "0.5 - 48.6 (23.2)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.3"
D372V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TEC MUTATED         0        2        3         1         3          1
  TEC WILD-TYPE       4      121      130        45        64         69
               vv
clus            STAGE IIIB STAGE IV
  TEC MUTATED            0        1
  TEC WILD-TYPE         11       24
D372V3, multiclass
            clus
vv           TEC MUTATED TEC WILD-TYPE
  STAGE I              0             4
  STAGE IA             2           121
  STAGE IB             3           130
  STAGE IIA            1            45
  STAGE IIB            3            64
  STAGE IIIA           1            69
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TEC MUTATED     2   8   1   0
  TEC WILD-TYPE 153 253  42  18
D372V4, multiclass
    clus
vv   TEC MUTATED TEC WILD-TYPE
  T1           2           153
  T2           8           253
  T3           1            42
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  TEC MUTATED     7   3     1
  TEC WILD-TYPE 300  86    71
D372V5, multiclass
       clus
vv      TEC MUTATED TEC WILD-TYPE
  N0              7           300
  N1              3            86
  N2+N3           1            71
[1] 3 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
  TEC MUTATED     7   1
  TEC WILD-TYPE 320  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEC MUTATED      7    1
  TEC WILD-TYPE  320   22
   clus
vv  TEC MUTATED TEC WILD-TYPE
  0           7           320
  1           1            22
[1] 2 2
[1] FALSE
D372V7, binary
               cls
clus              0   1
  TEC MUTATED     6   5
  TEC WILD-TYPE 253 216
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEC MUTATED      6    5
  TEC WILD-TYPE  253  216
        clus
vv       TEC MUTATED TEC WILD-TYPE
  FEMALE           6           253
  MALE             5           216
[1] 2 2
[1] FALSE
D372V8, continuous
[1] "Remove cluster labels:" "TEC MUTATED"           
clus
  TEC MUTATED TEC WILD-TYPE 
            2            82 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-53-A4EZ    TCGA-55-7283 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-55-7573    TCGA-55-7725    TCGA-55-7910    TCGA-55-7914    TCGA-55-8096 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-55-8205    TCGA-55-8208    TCGA-55-8507    TCGA-55-8508    TCGA-55-8511 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-55-8512    TCGA-55-8619    TCGA-55-8620    TCGA-55-A48Z    TCGA-55-A490 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-55-A494    TCGA-62-8394    TCGA-62-8395    TCGA-62-8397    TCGA-62-8398 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P    TCGA-62-A46R 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y    TCGA-62-A470 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681    TCGA-64-5778 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520    TCGA-73-4659 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4676    TCGA-73-7498 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-73-7499    TCGA-75-5122    TCGA-83-5908    TCGA-86-7701    TCGA-86-7711 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-86-7713    TCGA-86-7714    TCGA-86-7955    TCGA-86-8055    TCGA-86-8056 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-86-8074    TCGA-86-8075    TCGA-86-8076    TCGA-86-8278    TCGA-86-8279 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-86-8281    TCGA-86-8358    TCGA-86-8359    TCGA-86-8668    TCGA-86-8669 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-86-8671    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6849    TCGA-93-7348 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO    TCGA-99-7458    TCGA-MN-A4N1 
"TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" "TEC WILD-TYPE" 
   TCGA-MN-A4N4    TCGA-MN-A4N5 
"TEC WILD-TYPE" "TEC WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TEC MUTATED                            0                                 2
  TEC WILD-TYPE                         18                               100
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TEC MUTATED                                                    6
  TEC WILD-TYPE                                                288
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TEC MUTATED                                            0
  TEC WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TEC MUTATED                                               2
  TEC WILD-TYPE                                            17
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  TEC MUTATED                                1
  TEC WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  TEC MUTATED                                    0                            0
  TEC WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  TEC MUTATED                               0
  TEC WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TEC MUTATED                                               0
  TEC WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  TEC MUTATED                              0
  TEC WILD-TYPE                            9
D372V9, multiclass
                                                    clus
vv                                                   TEC MUTATED TEC WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            2           100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           6           288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                2            17
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V10, binary
               cls
clus              0   1
  TEC MUTATED     1  10
  TEC WILD-TYPE  19 450
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEC MUTATED      1   10
  TEC WILD-TYPE   19  450
     clus
vv    TEC MUTATED TEC WILD-TYPE
  NO            1            19
  YES          10           450
[1] 2 2
[1] FALSE
D372V11, continuous
D372V12, continuous
               vv
clus             R0  R1  R2  RX
  TEC MUTATED     7   0   0   1
  TEC WILD-TYPE 303  11   4  24
D372V13, multiclass
    clus
vv   TEC MUTATED TEC WILD-TYPE
  R0           7           303
  R1           0            11
  R2           0             4
  RX           1            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEC MUTATED                                  0     1
  TEC WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TEC MUTATED                           0     9
  TEC WILD-TYPE                        29   368
D372V14, multiclass
                                  clus
vv                                 TEC MUTATED TEC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                      9           368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V15, binary
               cls
clus              0   1
  TEC MUTATED     2   6
  TEC WILD-TYPE   4 343
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEC MUTATED      2    6
  TEC WILD-TYPE    4  343
                        clus
vv                       TEC MUTATED TEC WILD-TYPE
  HISPANIC OR LATINO               2             4
  NOT HISPANIC OR LATINO           6           343
[1] 2 2
[1] FALSE

Clustering(373) Variable = MARCH6 MUTATION ANALYSIS
D373V1, survival
                  sevent
clus2                0   1
  MARCH6 MUTATED    12   0
  MARCH6 WILD-TYPE 303 141
  MARCH6 MUTATED MARCH6 WILD-TYPE 
              12              444 
  MARCH6 MUTATED MARCH6 WILD-TYPE 
               0              141 
$`MARCH6 MUTATED`
TCGA-05-4382 TCGA-38-4626 TCGA-44-3918 TCGA-44-7660 TCGA-44-7661 TCGA-55-8094 
       19.96       120.79        34.06        19.46        12.03         0.13 
TCGA-55-8506 TCGA-55-A493 TCGA-73-4662 TCGA-86-6851 TCGA-97-7937 TCGA-99-7458 
        0.36         0.92        29.98         5.88         5.95        24.56 

$`MARCH6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
        2.04         7.40         5.98         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       14.60         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
        7.04         2.01         0.10        52.60        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79        25.48         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 
       20.52        17.75        20.84        18.67        20.68        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MARCH6 MUTATED MARCH6 WILD-TYPE 
            0.13             0.00 
  MARCH6 MUTATED MARCH6 WILD-TYPE 
          120.79           223.96 
  MARCH6 MUTATED MARCH6 WILD-TYPE 
          15.745           18.030 
[1] "0.1 - 120.8 (15.7)" "0.0 - 224.0 (18.0)"
[1] "hr="     "9600000"
D373V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MARCH6 MUTATED         0        2        6         2         1          1
  MARCH6 WILD-TYPE       4      121      127        44        66         69
                  vv
clus               STAGE IIIB STAGE IV
  MARCH6 MUTATED            0        1
  MARCH6 WILD-TYPE         11       24
D373V3, multiclass
            clus
vv           MARCH6 MUTATED MARCH6 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                6              127
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MARCH6 MUTATED     3   8   1   1
  MARCH6 WILD-TYPE 152 253  42  17
D373V4, multiclass
    clus
vv   MARCH6 MUTATED MARCH6 WILD-TYPE
  T1              3              152
  T2              8              253
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  MARCH6 MUTATED    12   1     0
  MARCH6 WILD-TYPE 295  88    72
D373V5, multiclass
       clus
vv      MARCH6 MUTATED MARCH6 WILD-TYPE
  N0                12              295
  N1                 1               88
  N2+N3              0               72
[1] 3 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
  MARCH6 MUTATED     9   1
  MARCH6 WILD-TYPE 318  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH6 MUTATED      9    1
  MARCH6 WILD-TYPE  318   22
   clus
vv  MARCH6 MUTATED MARCH6 WILD-TYPE
  0              9              318
  1              1               22
[1] 2 2
[1] FALSE
D373V7, binary
                  cls
clus                 0   1
  MARCH6 MUTATED     8   5
  MARCH6 WILD-TYPE 251 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH6 MUTATED      8    5
  MARCH6 WILD-TYPE  251  216
        clus
vv       MARCH6 MUTATED MARCH6 WILD-TYPE
  FEMALE              8              251
  MALE                5              216
[1] 2 2
[1] FALSE
D373V8, continuous
[1] "Remove cluster labels:" "MARCH6 MUTATED"        
clus
  MARCH6 MUTATED MARCH6 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4666       TCGA-73-4668 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-7955       TCGA-86-8055 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8281       TCGA-86-8358 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-MN-A4N1 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"MARCH6 WILD-TYPE" "MARCH6 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MARCH6 MUTATED                            0                                 2
  MARCH6 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MARCH6 MUTATED                                                    9
  MARCH6 WILD-TYPE                                                285
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MARCH6 MUTATED                                            0
  MARCH6 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MARCH6 MUTATED                                               1
  MARCH6 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  MARCH6 MUTATED                                0
  MARCH6 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  MARCH6 MUTATED                                    1
  MARCH6 WILD-TYPE                                  2
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MARCH6 MUTATED                              0                             0
  MARCH6 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MARCH6 MUTATED                                               0
  MARCH6 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  MARCH6 MUTATED                              0
  MARCH6 WILD-TYPE                            9
D373V9, multiclass
                                                    clus
vv                                                   MARCH6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              1
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   MARCH6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V10, binary
                  cls
clus                 0   1
  MARCH6 MUTATED     0  13
  MARCH6 WILD-TYPE  20 447
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH6 MUTATED      0   13
  MARCH6 WILD-TYPE   20  447
     clus
vv    MARCH6 MUTATED MARCH6 WILD-TYPE
  NO               0               20
  YES             13              447
[1] 2 2
[1] FALSE
D373V11, continuous
D373V12, continuous
                  vv
clus                R0  R1  R2  RX
  MARCH6 MUTATED     9   0   0   0
  MARCH6 WILD-TYPE 301  11   4  25
D373V13, multiclass
    clus
vv   MARCH6 MUTATED MARCH6 WILD-TYPE
  R0              9              301
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MARCH6 MUTATED                                  0     0
  MARCH6 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MARCH6 MUTATED                           0    11
  MARCH6 WILD-TYPE                        29   366
D373V14, multiclass
                                  clus
vv                                 MARCH6 MUTATED MARCH6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        11              366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V15, binary
                  cls
clus                 0   1
  MARCH6 MUTATED     0  11
  MARCH6 WILD-TYPE   6 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH6 MUTATED      0   11
  MARCH6 WILD-TYPE    6  338
                        clus
vv                       MARCH6 MUTATED MARCH6 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(374) Variable = AIFM3 MUTATION ANALYSIS
D374V1, survival
                 sevent
clus2               0   1
  AIFM3 MUTATED     4   2
  AIFM3 WILD-TYPE 311 139
  AIFM3 MUTATED AIFM3 WILD-TYPE 
              6             450 
  AIFM3 MUTATED AIFM3 WILD-TYPE 
              2             139 
$`AIFM3 MUTATED`
TCGA-44-5644 TCGA-55-8302 TCGA-55-8506 TCGA-78-7155 TCGA-MP-A4TF TCGA-NJ-A55R 
       28.37         0.76         0.36        38.50        11.05        19.82 

$`AIFM3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.42         1.45         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.13         1.64        29.13         0.26         0.43        59.11 

  AIFM3 MUTATED AIFM3 WILD-TYPE 
           0.36            0.00 
  AIFM3 MUTATED AIFM3 WILD-TYPE 
          38.50          223.96 
  AIFM3 MUTATED AIFM3 WILD-TYPE 
         15.435          18.030 
[1] "0.4 - 38.5 (15.4)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D374V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AIFM3 MUTATED         0        1        3         1         1          0
  AIFM3 WILD-TYPE       4      122      130        45        66         70
                 vv
clus              STAGE IIIB STAGE IV
  AIFM3 MUTATED            0        0
  AIFM3 WILD-TYPE         11       25
D374V3, multiclass
            clus
vv           AIFM3 MUTATED AIFM3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              1              45
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AIFM3 MUTATED     1   4   1   0
  AIFM3 WILD-TYPE 154 257  42  18
D374V4, multiclass
    clus
vv   AIFM3 MUTATED AIFM3 WILD-TYPE
  T1             1             154
  T2             4             257
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  AIFM3 MUTATED     6   0     0
  AIFM3 WILD-TYPE 301  89    72
D374V5, multiclass
       clus
vv      AIFM3 MUTATED AIFM3 WILD-TYPE
  N0                6             301
  N1                0              89
  N2+N3             0              72
[1] 3 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
  AIFM3 MUTATED     2   0
  AIFM3 WILD-TYPE 325  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM3 MUTATED      2    0
  AIFM3 WILD-TYPE  325   23
   clus
vv  AIFM3 MUTATED AIFM3 WILD-TYPE
  0             2             325
  1             0              23
[1] 2 2
[1] FALSE
D374V7, binary
                 cls
clus                0   1
  AIFM3 MUTATED     3   3
  AIFM3 WILD-TYPE 256 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM3 MUTATED      3    3
  AIFM3 WILD-TYPE  256  218
        clus
vv       AIFM3 MUTATED AIFM3 WILD-TYPE
  FEMALE             3             256
  MALE               3             218
[1] 2 2
[1] FALSE
D374V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AIFM3 MUTATED                            0                                 0
  AIFM3 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AIFM3 MUTATED                                                    6
  AIFM3 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AIFM3 MUTATED                                            0
  AIFM3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AIFM3 MUTATED                                               0
  AIFM3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  AIFM3 MUTATED                                0
  AIFM3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  AIFM3 MUTATED                                    0
  AIFM3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  AIFM3 MUTATED                              0                             0
  AIFM3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AIFM3 MUTATED                                               0
  AIFM3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  AIFM3 MUTATED                              0
  AIFM3 WILD-TYPE                            9
D374V9, multiclass
                                                    clus
vv                                                   AIFM3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   AIFM3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V10, binary
                 cls
clus                0   1
  AIFM3 MUTATED     0   6
  AIFM3 WILD-TYPE  20 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM3 MUTATED      0    6
  AIFM3 WILD-TYPE   20  454
     clus
vv    AIFM3 MUTATED AIFM3 WILD-TYPE
  NO              0              20
  YES             6             454
[1] 2 2
[1] FALSE
D374V11, continuous
D374V12, continuous
                 vv
clus               R0  R1  R2  RX
  AIFM3 MUTATED     4   0   0   0
  AIFM3 WILD-TYPE 306  11   4  25
D374V13, multiclass
    clus
vv   AIFM3 MUTATED AIFM3 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AIFM3 MUTATED                                  0     0
  AIFM3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AIFM3 MUTATED                           0     6
  AIFM3 WILD-TYPE                        29   371
D374V14, multiclass
                                  clus
vv                                 AIFM3 MUTATED AIFM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V15, binary
                 cls
clus                0   1
  AIFM3 MUTATED     0   4
  AIFM3 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM3 MUTATED      0    4
  AIFM3 WILD-TYPE    6  345
                        clus
vv                       AIFM3 MUTATED AIFM3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(375) Variable = MSRB2 MUTATION ANALYSIS
D375V1, survival
                 sevent
clus2               0   1
  MSRB2 MUTATED     4   2
  MSRB2 WILD-TYPE 311 139
  MSRB2 MUTATED MSRB2 WILD-TYPE 
              6             450 
  MSRB2 MUTATED MSRB2 WILD-TYPE 
              2             139 
$`MSRB2 MUTATED`
TCGA-05-4382 TCGA-05-5420 TCGA-44-4112 TCGA-69-7979 TCGA-86-A4JF TCGA-97-7938 
       19.96        15.02        26.56         2.93        17.62         0.59 

$`MSRB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24        34.06         6.25        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       16.70        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32        13.32        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79        25.48         5.95         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MSRB2 MUTATED MSRB2 WILD-TYPE 
           0.59            0.00 
  MSRB2 MUTATED MSRB2 WILD-TYPE 
          26.56          223.96 
  MSRB2 MUTATED MSRB2 WILD-TYPE 
          16.32           18.10 
[1] "0.6 - 26.6 (16.3)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "2.2"
D375V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MSRB2 MUTATED         0        1        3         0         1          1
  MSRB2 WILD-TYPE       4      122      130        46        66         69
                 vv
clus              STAGE IIIB STAGE IV
  MSRB2 MUTATED            0        0
  MSRB2 WILD-TYPE         11       25
D375V3, multiclass
            clus
vv           MSRB2 MUTATED MSRB2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MSRB2 MUTATED     1   4   1   0
  MSRB2 WILD-TYPE 154 257  42  18
D375V4, multiclass
    clus
vv   MSRB2 MUTATED MSRB2 WILD-TYPE
  T1             1             154
  T2             4             257
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  MSRB2 MUTATED     5   0     1
  MSRB2 WILD-TYPE 302  89    71
D375V5, multiclass
       clus
vv      MSRB2 MUTATED MSRB2 WILD-TYPE
  N0                5             302
  N1                0              89
  N2+N3             1              71
[1] 3 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
  MSRB2 MUTATED     4   0
  MSRB2 WILD-TYPE 323  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSRB2 MUTATED      4    0
  MSRB2 WILD-TYPE  323   23
   clus
vv  MSRB2 MUTATED MSRB2 WILD-TYPE
  0             4             323
  1             0              23
[1] 2 2
[1] FALSE
D375V7, binary
                 cls
clus                0   1
  MSRB2 MUTATED     3   3
  MSRB2 WILD-TYPE 256 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSRB2 MUTATED      3    3
  MSRB2 WILD-TYPE  256  218
        clus
vv       MSRB2 MUTATED MSRB2 WILD-TYPE
  FEMALE             3             256
  MALE               3             218
[1] 2 2
[1] FALSE
D375V8, continuous
[1] "Remove cluster labels:" "MSRB2 MUTATED"         
clus
  MSRB2 MUTATED MSRB2 WILD-TYPE 
              1              83 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-A48Z 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-73-7498      TCGA-73-7499 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-7701      TCGA-86-7711 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7954      TCGA-86-7955 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8074      TCGA-86-8075 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8281 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" "MSRB2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MSRB2 MUTATED                            1                                 1
  MSRB2 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MSRB2 MUTATED                                                    3
  MSRB2 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MSRB2 MUTATED                                            0
  MSRB2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MSRB2 MUTATED                                               1
  MSRB2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  MSRB2 MUTATED                                0
  MSRB2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  MSRB2 MUTATED                                    0
  MSRB2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MSRB2 MUTATED                              0                             0
  MSRB2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MSRB2 MUTATED                                               0
  MSRB2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  MSRB2 MUTATED                              0
  MSRB2 WILD-TYPE                            9
D375V9, multiclass
                                                    clus
vv                                                   MSRB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   MSRB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V10, binary
                 cls
clus                0   1
  MSRB2 MUTATED     0   6
  MSRB2 WILD-TYPE  20 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSRB2 MUTATED      0    6
  MSRB2 WILD-TYPE   20  454
     clus
vv    MSRB2 MUTATED MSRB2 WILD-TYPE
  NO              0              20
  YES             6             454
[1] 2 2
[1] FALSE
D375V11, continuous
D375V12, continuous
                 vv
clus               R0  R1  R2  RX
  MSRB2 MUTATED     5   0   0   0
  MSRB2 WILD-TYPE 305  11   4  25
D375V13, multiclass
    clus
vv   MSRB2 MUTATED MSRB2 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSRB2 MUTATED                                  0     0
  MSRB2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MSRB2 MUTATED                           0     4
  MSRB2 WILD-TYPE                        29   373
D375V14, multiclass
                                  clus
vv                                 MSRB2 MUTATED MSRB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V15, binary
                 cls
clus                0   1
  MSRB2 MUTATED     0   4
  MSRB2 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSRB2 MUTATED      0    4
  MSRB2 WILD-TYPE    6  345
                        clus
vv                       MSRB2 MUTATED MSRB2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(376) Variable = KDM3B MUTATION ANALYSIS
D376V1, survival
                 sevent
clus2               0   1
  KDM3B MUTATED     8   5
  KDM3B WILD-TYPE 307 136
  KDM3B MUTATED KDM3B WILD-TYPE 
             13             443 
  KDM3B MUTATED KDM3B WILD-TYPE 
              5             136 
$`KDM3B MUTATED`
TCGA-44-3918 TCGA-50-5936 TCGA-55-1595 TCGA-55-6982 TCGA-55-8620 TCGA-62-A46Y 
       34.06         8.45        48.62        32.71         2.17        13.61 
TCGA-69-7980 TCGA-73-4677 TCGA-86-6851 TCGA-91-6831 TCGA-95-7039 TCGA-MP-A4TH 
       12.56         1.25         5.88        10.19         1.12        14.66 
TCGA-MP-A4TI 
       14.10 

$`KDM3B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       24.36        42.77        37.15        38.24         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        78.67        21.47        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        23.05         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
        5.49         7.79         2.20        45.34        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30         2.93        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        6.12        23.61         1.08        19.00        17.29         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  KDM3B MUTATED KDM3B WILD-TYPE 
           1.12            0.00 
  KDM3B MUTATED KDM3B WILD-TYPE 
          48.62          223.96 
  KDM3B MUTATED KDM3B WILD-TYPE 
          12.56           18.64 
[1] "1.1 - 48.6 (12.6)"  "0.0 - 224.0 (18.6)"
[1] "hr=" "2"  
D376V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KDM3B MUTATED         1        4        1         2         2          3
  KDM3B WILD-TYPE       3      119      132        44        65         67
                 vv
clus              STAGE IIIB STAGE IV
  KDM3B MUTATED            0        1
  KDM3B WILD-TYPE         11       24
D376V3, multiclass
            clus
vv           KDM3B MUTATED KDM3B WILD-TYPE
  STAGE I                1               3
  STAGE IA               4             119
  STAGE IB               1             132
  STAGE IIA              2              44
  STAGE IIB              2              65
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of 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     6   6   2   0
  KDM3B WILD-TYPE 149 255  41  18
D376V4, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  T1             6             149
  T2             6             255
  T3             2              41
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  KDM3B MUTATED     7   4     3
  KDM3B WILD-TYPE 300  85    69
D376V5, multiclass
       clus
vv      KDM3B MUTATED KDM3B WILD-TYPE
  N0                7             300
  N1                4              85
  N2+N3             3              69
[1] 3 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
  KDM3B MUTATED    11   1
  KDM3B WILD-TYPE 316  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     11    1
  KDM3B WILD-TYPE  316   22
   clus
vv  KDM3B MUTATED KDM3B WILD-TYPE
  0            11             316
  1             1              22
[1] 2 2
[1] FALSE
D376V7, binary
                 cls
clus                0   1
  KDM3B MUTATED     9   5
  KDM3B WILD-TYPE 250 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED      9    5
  KDM3B WILD-TYPE  250  216
        clus
vv       KDM3B MUTATED KDM3B WILD-TYPE
  FEMALE             9             250
  MALE               5             216
[1] 2 2
[1] FALSE
D376V8, continuous
[1] "Remove cluster labels:" "KDM3B MUTATED"         
clus
  KDM3B MUTATED KDM3B WILD-TYPE 
              2              82 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-53-A4EZ 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-A48Z      TCGA-55-A490 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5778      TCGA-69-7974 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4676 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8055      TCGA-86-8056 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A4JF 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-86-A4P7      TCGA-91-6849      TCGA-93-7348      TCGA-93-8067 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-99-7458      TCGA-MN-A4N1 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KDM3B MUTATED                            0                                 3
  KDM3B WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KDM3B MUTATED                                                    8
  KDM3B WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KDM3B MUTATED                                            0
  KDM3B WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KDM3B MUTATED                                               0
  KDM3B WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KDM3B MUTATED                                1
  KDM3B WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KDM3B MUTATED                                    0
  KDM3B WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KDM3B MUTATED                              0                             1
  KDM3B WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KDM3B MUTATED                                               0
  KDM3B WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KDM3B MUTATED                              1
  KDM3B WILD-TYPE                            8
D376V9, multiclass
                                                    clus
vv                                                   KDM3B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   KDM3B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V10, binary
                 cls
clus                0   1
  KDM3B MUTATED     0  14
  KDM3B WILD-TYPE  20 446
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED      0   14
  KDM3B WILD-TYPE   20  446
     clus
vv    KDM3B MUTATED KDM3B WILD-TYPE
  NO              0              20
  YES            14             446
[1] 2 2
[1] FALSE
D376V11, continuous
D376V12, continuous
                 vv
clus               R0  R1  R2  RX
  KDM3B MUTATED     6   0   1   0
  KDM3B WILD-TYPE 304  11   3  25
D376V13, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  R0             6             304
  R1             0              11
  R2             1               3
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM3B MUTATED                                  0     1
  KDM3B WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM3B MUTATED                           0    12
  KDM3B WILD-TYPE                        29   365
D376V14, multiclass
                                  clus
vv                                 KDM3B MUTATED KDM3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       12             365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V15, binary
                 cls
clus                0   1
  KDM3B MUTATED     0  12
  KDM3B WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED      0   12
  KDM3B WILD-TYPE    6  337
                        clus
vv                       KDM3B MUTATED KDM3B WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(377) Variable = THPO MUTATION ANALYSIS
D377V1, survival
                sevent
clus2              0   1
  THPO MUTATED     3   4
  THPO WILD-TYPE 312 137
  THPO MUTATED THPO WILD-TYPE 
             7            449 
  THPO MUTATED THPO WILD-TYPE 
             4            137 
$`THPO MUTATED`
TCGA-55-7994 TCGA-55-8096 TCGA-55-8205 TCGA-55-A4DF TCGA-78-8662 TCGA-86-8672 
       19.82        23.64         1.08        20.19       110.50         0.62 
TCGA-J2-A4AE 
       35.47 

$`THPO WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
        3.29        19.66        19.73         5.06         0.13        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        0.10        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31         1.32         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       24.49         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
        1.15        13.91        30.84        27.58        14.96        13.32 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  THPO MUTATED THPO WILD-TYPE 
          0.62           0.00 
  THPO MUTATED THPO WILD-TYPE 
        110.50         223.96 
  THPO MUTATED THPO WILD-TYPE 
         20.19          17.92 
[1] "0.6 - 110.5 (20.2)" "0.0 - 224.0 (17.9)"
[1] "hr=" "1.3"
D377V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  THPO MUTATED         0        3        2         0         3          0
  THPO WILD-TYPE       4      120      131        46        64         70
                vv
clus             STAGE IIIB STAGE IV
  THPO MUTATED            0        0
  THPO WILD-TYPE         11       25
D377V3, multiclass
            clus
vv           THPO MUTATED THPO WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              2            131
  STAGE IIA             0             46
  STAGE IIB             3             64
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  THPO MUTATED     3   3   2   0
  THPO WILD-TYPE 152 258  41  18
D377V4, multiclass
    clus
vv   THPO MUTATED THPO WILD-TYPE
  T1            3            152
  T2            3            258
  T3            2             41
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  THPO MUTATED     7   0     0
  THPO WILD-TYPE 300  89    72
D377V5, multiclass
       clus
vv      THPO MUTATED THPO WILD-TYPE
  N0               7            300
  N1               0             89
  N2+N3            0             72
[1] 3 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
  THPO MUTATED     4   0
  THPO WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  THPO MUTATED      4    0
  THPO WILD-TYPE  323   23
   clus
vv  THPO MUTATED THPO WILD-TYPE
  0            4            323
  1            0             23
[1] 2 2
[1] FALSE
D377V7, binary
                cls
clus               0   1
  THPO MUTATED     4   4
  THPO WILD-TYPE 255 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  THPO MUTATED      4    4
  THPO WILD-TYPE  255  217
        clus
vv       THPO MUTATED THPO WILD-TYPE
  FEMALE            4            255
  MALE              4            217
[1] 2 2
[1] FALSE
D377V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  THPO MUTATED                            0                                 0
  THPO WILD-TYPE                         18                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  THPO MUTATED                                                    8
  THPO WILD-TYPE                                                286
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  THPO MUTATED                                            0
  THPO WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  THPO MUTATED                                               0
  THPO WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  THPO MUTATED                                0
  THPO WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  THPO MUTATED                                    0
  THPO WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  THPO MUTATED                              0                             0
  THPO WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  THPO MUTATED                                               0
  THPO WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  THPO MUTATED                              0
  THPO WILD-TYPE                            9
D377V9, multiclass
                                                    clus
vv                                                   THPO MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   THPO WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V10, binary
                cls
clus               0   1
  THPO MUTATED     0   8
  THPO WILD-TYPE  20 452
[1] "tbl2"
                cls
clus             [,1] [,2]
  THPO MUTATED      0    8
  THPO WILD-TYPE   20  452
     clus
vv    THPO MUTATED THPO WILD-TYPE
  NO             0             20
  YES            8            452
[1] 2 2
[1] FALSE
D377V11, continuous
D377V12, continuous
                vv
clus              R0  R1  R2  RX
  THPO MUTATED     6   0   0   0
  THPO WILD-TYPE 304  11   4  25
D377V13, multiclass
    clus
vv   THPO MUTATED THPO WILD-TYPE
  R0            6            304
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THPO MUTATED                                  0     0
  THPO WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  THPO MUTATED                           0     7
  THPO WILD-TYPE                        29   370
D377V14, multiclass
                                  clus
vv                                 THPO MUTATED THPO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V15, binary
                cls
clus               0   1
  THPO MUTATED     0   7
  THPO WILD-TYPE   6 342
[1] "tbl2"
                cls
clus             [,1] [,2]
  THPO MUTATED      0    7
  THPO WILD-TYPE    6  342
                        clus
vv                       THPO MUTATED THPO WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            7            342
[1] 2 2
[1] FALSE

Clustering(378) Variable = CACNA1F MUTATION ANALYSIS
D378V1, survival
                   sevent
clus2                 0   1
  CACNA1F MUTATED    18   8
  CACNA1F WILD-TYPE 297 133
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               26               430 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
                8               133 
$`CACNA1F MUTATED`
TCGA-05-4402 TCGA-38-4631 TCGA-44-A4SS TCGA-49-4514 TCGA-49-6743 TCGA-50-5045 
        8.02        11.64        13.64        55.89        12.13        71.47 
TCGA-53-A4EZ TCGA-55-7281 TCGA-55-8203 TCGA-55-8301 TCGA-55-8511 TCGA-55-A48X 
        9.21         0.59        17.98         1.45         0.30        22.65 
TCGA-62-A46R TCGA-64-5778 TCGA-64-5815 TCGA-69-7979 TCGA-69-A59K TCGA-78-7147 
       56.71        42.90        28.47         2.93         7.04        19.27 
TCGA-78-7166 TCGA-78-7220 TCGA-91-8497 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7941 
        8.48        26.53        14.27        18.18        31.69         0.72 
TCGA-L9-A444 TCGA-MN-A4N4 
        0.20        38.63 

$`CACNA1F WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       14.63        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1.74         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
        1.08         1.51         2.17        22.16        15.42         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
        0.95         0.36         0.26         0.49        17.72         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        16.93        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 
       87.98         2.04        28.41        51.25        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 
       12.56        14.01        13.45         4.24         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
       22.29         7.07       104.19       223.96        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7547 
       15.65        27.29         2.76        21.40        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 
       63.52        43.79        25.48         5.95         0.59        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 
       35.47        16.44        19.00        14.30         3.81        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  CACNA1F MUTATED CACNA1F WILD-TYPE 
              0.2               0.0 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
            71.47            223.96 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
           13.955            18.380 
[1] "0.2 - 71.5 (14.0)"  "0.0 - 224.0 (18.4)"
[1] "hr=" "1.1"
D378V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CACNA1F MUTATED         0        9        7         3         4          3
  CACNA1F WILD-TYPE       4      114      126        43        63         67
                   vv
clus                STAGE IIIB STAGE IV
  CACNA1F MUTATED            0        1
  CACNA1F WILD-TYPE         11       24
D378V3, multiclass
            clus
vv           CACNA1F MUTATED CACNA1F WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 9               114
  STAGE IB                 7               126
  STAGE IIA                3                43
  STAGE IIB                4                63
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CACNA1F MUTATED    11  15   1   0
  CACNA1F WILD-TYPE 144 246  42  18
D378V4, multiclass
    clus
vv   CACNA1F MUTATED CACNA1F WILD-TYPE
  T1              11               144
  T2              15               246
  T3               1                42
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  CACNA1F MUTATED    16   7     3
  CACNA1F WILD-TYPE 291  82    69
D378V5, multiclass
       clus
vv      CACNA1F MUTATED CACNA1F WILD-TYPE
  N0                 16               291
  N1                  7                82
  N2+N3               3                69
[1] 3 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
  CACNA1F MUTATED    16   1
  CACNA1F WILD-TYPE 311  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED     16    1
  CACNA1F WILD-TYPE  311   22
   clus
vv  CACNA1F MUTATED CACNA1F WILD-TYPE
  0              16               311
  1               1                22
[1] 2 2
[1] FALSE
D378V7, binary
                   cls
clus                  0   1
  CACNA1F MUTATED    20   7
  CACNA1F WILD-TYPE 239 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED     20    7
  CACNA1F WILD-TYPE  239  214
        clus
vv       CACNA1F MUTATED CACNA1F WILD-TYPE
  FEMALE              20               239
  MALE                 7               214
[1] 2 2
[1] FALSE
D378V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  CACNA1F MUTATED                            4
  CACNA1F WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  CACNA1F MUTATED                                   5
  CACNA1F WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CACNA1F MUTATED                                                   14
  CACNA1F WILD-TYPE                                                280
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CACNA1F MUTATED                                            0
  CACNA1F WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CACNA1F MUTATED                                               1
  CACNA1F WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  CACNA1F MUTATED                                1
  CACNA1F WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  CACNA1F MUTATED                                    0
  CACNA1F WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CACNA1F MUTATED                              0                             1
  CACNA1F WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CACNA1F MUTATED                                               1
  CACNA1F WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  CACNA1F MUTATED                              0
  CACNA1F WILD-TYPE                            9
D378V9, multiclass
                                                    clus
vv                                                   CACNA1F MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              14
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   CACNA1F WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V10, binary
                   cls
clus                  0   1
  CACNA1F MUTATED     3  24
  CACNA1F WILD-TYPE  17 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED      3   24
  CACNA1F WILD-TYPE   17  436
     clus
vv    CACNA1F MUTATED CACNA1F WILD-TYPE
  NO                3                17
  YES              24               436
[1] 2 2
[1] FALSE
D378V11, continuous
D378V12, continuous
                   vv
clus                 R0  R1  R2  RX
  CACNA1F MUTATED    19   0   1   1
  CACNA1F WILD-TYPE 291  11   3  24
D378V13, multiclass
    clus
vv   CACNA1F MUTATED CACNA1F WILD-TYPE
  R0              19               291
  R1               0                11
  R2               1                 3
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA1F MUTATED                                  0     0
  CACNA1F WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CACNA1F MUTATED                           2    23
  CACNA1F WILD-TYPE                        27   354
D378V14, multiclass
                                  clus
vv                                 CACNA1F MUTATED CACNA1F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         23               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V15, binary
                   cls
clus                  0   1
  CACNA1F MUTATED     1  18
  CACNA1F WILD-TYPE   5 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED      1   18
  CACNA1F WILD-TYPE    5  331
                        clus
vv                       CACNA1F MUTATED CACNA1F WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              18               331
[1] 2 2
[1] FALSE

Clustering(379) Variable = SELE MUTATION ANALYSIS
D379V1, survival
                sevent
clus2              0   1
  SELE MUTATED     9   1
  SELE WILD-TYPE 306 140
  SELE MUTATED SELE WILD-TYPE 
            10            446 
  SELE MUTATED SELE WILD-TYPE 
             1            140 
$`SELE MUTATED`
TCGA-49-6742 TCGA-53-7624 TCGA-55-8089 TCGA-64-5781 TCGA-69-8253 TCGA-86-8074 
       14.63        34.29         3.29        51.25        14.01         0.79 
TCGA-86-A4JF TCGA-91-6848 TCGA-97-7553 TCGA-99-8028 
       17.62         7.36        43.79        36.76 

$`SELE WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        55.43        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        28.47        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       12.56        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57        24.33        15.75        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
       19.89        31.69        64.60        63.52        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        34.85         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  SELE MUTATED SELE WILD-TYPE 
          0.79           0.00 
  SELE MUTATED SELE WILD-TYPE 
         51.25         223.96 
  SELE MUTATED SELE WILD-TYPE 
        16.125         18.100 
[1] "0.8 - 51.2 (16.1)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "3.1"
D379V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SELE MUTATED         0        3        3         2         2          1
  SELE WILD-TYPE       4      120      130        44        65         69
                vv
clus             STAGE IIIB STAGE IV
  SELE MUTATED            0        1
  SELE WILD-TYPE         11       24
D379V3, multiclass
            clus
vv           SELE MUTATED SELE WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              3            130
  STAGE IIA             2             44
  STAGE IIB             2             65
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SELE MUTATED     5   6   1   0
  SELE WILD-TYPE 150 255  42  18
D379V4, multiclass
    clus
vv   SELE MUTATED SELE WILD-TYPE
  T1            5            150
  T2            6            255
  T3            1             42
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  SELE MUTATED     8   3     1
  SELE WILD-TYPE 299  86    71
D379V5, multiclass
       clus
vv      SELE MUTATED SELE WILD-TYPE
  N0               8            299
  N1               3             86
  N2+N3            1             71
[1] 3 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
  SELE MUTATED     7   1
  SELE WILD-TYPE 320  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELE MUTATED      7    1
  SELE WILD-TYPE  320   22
   clus
vv  SELE MUTATED SELE WILD-TYPE
  0            7            320
  1            1             22
[1] 2 2
[1] FALSE
D379V7, binary
                cls
clus               0   1
  SELE MUTATED     7   5
  SELE WILD-TYPE 252 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELE MUTATED      7    5
  SELE WILD-TYPE  252  216
        clus
vv       SELE MUTATED SELE WILD-TYPE
  FEMALE            7            252
  MALE              5            216
[1] 2 2
[1] FALSE
D379V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SELE MUTATED                            0                                 2
  SELE WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SELE MUTATED                                                    8
  SELE WILD-TYPE                                                286
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SELE MUTATED                                            0
  SELE WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SELE MUTATED                                               1
  SELE WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SELE MUTATED                                0
  SELE WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SELE MUTATED                                    0
  SELE WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SELE MUTATED                              0                             0
  SELE WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SELE MUTATED                                               0
  SELE WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SELE MUTATED                              1
  SELE WILD-TYPE                            8
D379V9, multiclass
                                                    clus
vv                                                   SELE MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   SELE WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V10, binary
                cls
clus               0   1
  SELE MUTATED     0  12
  SELE WILD-TYPE  20 448
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELE MUTATED      0   12
  SELE WILD-TYPE   20  448
     clus
vv    SELE MUTATED SELE WILD-TYPE
  NO             0             20
  YES           12            448
[1] 2 2
[1] FALSE
D379V11, continuous
D379V12, continuous
                vv
clus              R0  R1  R2  RX
  SELE MUTATED     9   0   0   0
  SELE WILD-TYPE 301  11   4  25
D379V13, multiclass
    clus
vv   SELE MUTATED SELE WILD-TYPE
  R0            9            301
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SELE MUTATED                                  0     0
  SELE WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SELE MUTATED                           2     9
  SELE WILD-TYPE                        27   368
D379V14, multiclass
                                  clus
vv                                 SELE MUTATED SELE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                       9            368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V15, binary
                cls
clus               0   1
  SELE MUTATED     1  10
  SELE WILD-TYPE   5 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELE MUTATED      1   10
  SELE WILD-TYPE    5  339
                        clus
vv                       SELE MUTATED SELE WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(380) Variable = THY1 MUTATION ANALYSIS
D380V1, survival
                sevent
clus2              0   1
  THY1 MUTATED     4   1
  THY1 WILD-TYPE 311 140
  THY1 MUTATED THY1 WILD-TYPE 
             5            451 
  THY1 MUTATED THY1 WILD-TYPE 
             1            140 
$`THY1 MUTATED`
TCGA-50-5930 TCGA-55-7903 TCGA-69-7979 TCGA-86-8054 TCGA-91-6848 
        9.27        18.64         2.93        24.49         7.36 

$`THY1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        16.70         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  THY1 MUTATED THY1 WILD-TYPE 
          2.93           0.00 
  THY1 MUTATED THY1 WILD-TYPE 
         24.49         223.96 
  THY1 MUTATED THY1 WILD-TYPE 
          9.27          18.08 
[1] "2.9 - 24.5 (9.3)"   "0.0 - 224.0 (18.1)"
[1] "hr=" "1.5"
D380V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  THY1 MUTATED         0        1        1         0         1          2
  THY1 WILD-TYPE       4      122      132        46        66         68
                vv
clus             STAGE IIIB STAGE IV
  THY1 MUTATED            0        0
  THY1 WILD-TYPE         11       25
D380V3, multiclass
            clus
vv           THY1 MUTATED THY1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              1            132
  STAGE IIA             0             46
  STAGE IIB             1             66
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  THY1 MUTATED     1   4   0   0
  THY1 WILD-TYPE 154 257  43  18
D380V4, multiclass
    clus
vv   THY1 MUTATED THY1 WILD-TYPE
  T1            1            154
  T2            4            257
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  THY1 MUTATED     2   1     2
  THY1 WILD-TYPE 305  88    70
D380V5, multiclass
       clus
vv      THY1 MUTATED THY1 WILD-TYPE
  N0               2            305
  N1               1             88
  N2+N3            2             70
[1] 3 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
  THY1 MUTATED     2   0
  THY1 WILD-TYPE 325  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  THY1 MUTATED      2    0
  THY1 WILD-TYPE  325   23
   clus
vv  THY1 MUTATED THY1 WILD-TYPE
  0            2            325
  1            0             23
[1] 2 2
[1] FALSE
D380V7, binary
                cls
clus               0   1
  THY1 MUTATED     1   4
  THY1 WILD-TYPE 258 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  THY1 MUTATED      1    4
  THY1 WILD-TYPE  258  217
        clus
vv       THY1 MUTATED THY1 WILD-TYPE
  FEMALE            1            258
  MALE              4            217
[1] 2 2
[1] FALSE
D380V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  THY1 MUTATED                            2                                 1
  THY1 WILD-TYPE                         16                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  THY1 MUTATED                                                    2
  THY1 WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  THY1 MUTATED                                            0
  THY1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  THY1 MUTATED                                               0
  THY1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  THY1 MUTATED                                0
  THY1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  THY1 MUTATED                                    0
  THY1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  THY1 MUTATED                              0                             0
  THY1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  THY1 MUTATED                                               0
  THY1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  THY1 MUTATED                              0
  THY1 WILD-TYPE                            9
D380V9, multiclass
                                                    clus
vv                                                   THY1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   THY1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V10, binary
                cls
clus               0   1
  THY1 MUTATED     1   4
  THY1 WILD-TYPE  19 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  THY1 MUTATED      1    4
  THY1 WILD-TYPE   19  456
     clus
vv    THY1 MUTATED THY1 WILD-TYPE
  NO             1             19
  YES            4            456
[1] 2 2
[1] FALSE
D380V11, continuous
D380V12, continuous
[1] "Remove cluster labels:" "THY1 MUTATED"          
clus
  THY1 MUTATED THY1 WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     TCGA-44-3396 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-5644 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6147 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     TCGA-44-6776 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7661     TCGA-44-7662     TCGA-44-7667 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7670     TCGA-44-7672     TCGA-44-8117 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-1592     TCGA-55-1595     TCGA-55-5899     TCGA-55-6642 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-6712     TCGA-55-6971     TCGA-55-7227     TCGA-55-7283 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7728     TCGA-55-7907 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7914     TCGA-55-8089 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8615     TCGA-55-8620     TCGA-55-8621 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A493     TCGA-55-A494 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-62-8398     TCGA-64-1677     TCGA-64-1681     TCGA-64-5774 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-69-7761     TCGA-69-7763     TCGA-69-7764     TCGA-69-7765 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-7498 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7031 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7145     TCGA-78-7146     TCGA-78-7147     TCGA-78-7148 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7149     TCGA-78-7150     TCGA-78-7152     TCGA-78-7153 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7154     TCGA-78-7155     TCGA-78-7156     TCGA-78-7158 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7159     TCGA-78-7160     TCGA-78-7161     TCGA-78-7162 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7163     TCGA-78-7166     TCGA-78-7167     TCGA-78-7220 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7535     TCGA-78-7536     TCGA-78-7537     TCGA-78-7539 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-80-5608     TCGA-83-5908     TCGA-86-6851     TCGA-86-7711 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-8055     TCGA-86-8056 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6836 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  THY1 MUTATED     2   0   0   0
  THY1 WILD-TYPE 308  11   4  25
D380V13, multiclass
[1] "Remove cluster labels:" "THY1 MUTATED"          
clus
  THY1 MUTATED THY1 WILD-TYPE 
             2            348 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-4123 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-4627 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-38-4628     TCGA-38-4629     TCGA-38-4630     TCGA-38-4631 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-38-4632     TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-2657     TCGA-44-2661     TCGA-44-2665     TCGA-44-3396 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-3919     TCGA-44-4112 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6148     TCGA-44-6775     TCGA-44-A479 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-44-A47A     TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4494 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-49-4501     TCGA-49-4505     TCGA-49-4506     TCGA-49-4507 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-49-4510     TCGA-49-4512     TCGA-49-4514     TCGA-49-6742 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-49-6744     TCGA-49-6761     TCGA-49-6767     TCGA-50-5051 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-50-5055     TCGA-50-5066     TCGA-50-5931     TCGA-50-5942 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-50-5944     TCGA-50-6593     TCGA-50-6597     TCGA-50-6673 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-50-8460     TCGA-53-7624     TCGA-53-7626     TCGA-53-A4EZ 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-1592     TCGA-55-5899     TCGA-55-6642     TCGA-55-6970 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-6971     TCGA-55-6972     TCGA-55-6980     TCGA-55-6981 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-6983     TCGA-55-6985     TCGA-55-7281     TCGA-55-7284 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7727     TCGA-55-7728 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-7815     TCGA-55-7907     TCGA-55-7910     TCGA-55-7911 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-7994     TCGA-55-7995     TCGA-55-8085 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8087     TCGA-55-8089     TCGA-55-8090     TCGA-55-8091 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8097     TCGA-55-8203 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8204     TCGA-55-8205     TCGA-55-8206     TCGA-55-8207 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8505     TCGA-55-8506     TCGA-55-8507     TCGA-55-8508 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8510     TCGA-55-8511     TCGA-55-8512     TCGA-55-8513 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8614     TCGA-55-8615     TCGA-55-8616 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-55-A4DG     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1676     TCGA-64-1677     TCGA-64-1679 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5774     TCGA-64-5775     TCGA-64-5778 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-64-5779     TCGA-64-5781     TCGA-64-5815     TCGA-67-3771 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-67-3773     TCGA-67-4679     TCGA-67-6215     TCGA-67-6216 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-67-6217     TCGA-71-6725     TCGA-71-8520     TCGA-73-4658 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-4677 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-75-5125 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-75-5126     TCGA-75-5146     TCGA-75-5147     TCGA-75-6203 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-75-6205     TCGA-75-6206     TCGA-75-6207     TCGA-75-6211 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-75-6212     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-75-7030     TCGA-75-7031     TCGA-78-7143     TCGA-78-7145 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7540 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-80-5608     TCGA-80-5611     TCGA-83-5908     TCGA-86-6562 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-7953     TCGA-86-7954     TCGA-86-7955     TCGA-86-8055 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8585     TCGA-86-8668 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-8672     TCGA-86-8673 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-91-6828     TCGA-91-6829     TCGA-91-6835     TCGA-91-6840 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-7546 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-97-7554     TCGA-97-7938     TCGA-97-7941     TCGA-97-8176 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-99-8028     TCGA-99-8032     TCGA-99-8033     TCGA-J2-A4AD 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
    TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" "THY1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THY1 MUTATED                                  0     0
  THY1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  THY1 MUTATED                           0     5
  THY1 WILD-TYPE                        29   372
D380V14, multiclass
                                  clus
vv                                 THY1 MUTATED THY1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V15, binary
                cls
clus               0   1
  THY1 MUTATED     0   5
  THY1 WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  THY1 MUTATED      0    5
  THY1 WILD-TYPE    6  344
                        clus
vv                       THY1 MUTATED THY1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(381) Variable = TTK MUTATION ANALYSIS
D381V1, survival
               sevent
clus2             0   1
  TTK MUTATED    12   6
  TTK WILD-TYPE 303 135
  TTK MUTATED TTK WILD-TYPE 
           18           438 
  TTK MUTATED TTK WILD-TYPE 
            6           135 
$`TTK MUTATED`
TCGA-05-4382 TCGA-05-4398 TCGA-05-5420 TCGA-35-5375 TCGA-38-4625 TCGA-44-8120 
       19.96        47.05        15.02         8.68        97.74         8.55 
TCGA-50-5930 TCGA-50-6590 TCGA-55-7576 TCGA-55-8090 TCGA-55-8299 TCGA-67-6215 
        9.27        42.35         1.32        19.66        15.42         5.72 
TCGA-73-4659 TCGA-78-7145 TCGA-95-7039 TCGA-97-8172 TCGA-99-7458 TCGA-MN-A4N5 
       23.38        27.16         1.12        17.92        24.56         2.76 

$`TTK WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        5.98       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       13.15        24.36        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
       19.82         0.16        29.72        15.19         3.29        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        22.16         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6216 
       51.25        28.47        20.05        18.84        14.04         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
        1.25        39.09        23.51       163.10         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        0.20        27.19        38.63        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  TTK MUTATED TTK WILD-TYPE 
         1.12          0.00 
  TTK MUTATED TTK WILD-TYPE 
        97.74        223.96 
  TTK MUTATED TTK WILD-TYPE 
        16.67         18.10 
[1] "1.1 - 97.7 (16.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.2"
D381V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TTK MUTATED         0        3        7         0         1          5
  TTK WILD-TYPE       4      120      126        46        66         65
               vv
clus            STAGE IIIB STAGE IV
  TTK MUTATED            1        1
  TTK WILD-TYPE         10       24
D381V3, multiclass
            clus
vv           TTK MUTATED TTK WILD-TYPE
  STAGE I              0             4
  STAGE IA             3           120
  STAGE IB             7           126
  STAGE IIA            0            46
  STAGE IIB            1            66
  STAGE IIIA           5            65
  STAGE IIIB           1            10
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TTK MUTATED     3  11   1   3
  TTK WILD-TYPE 152 250  42  15
D381V4, multiclass
    clus
vv   TTK MUTATED TTK WILD-TYPE
  T1           3           152
  T2          11           250
  T3           1            42
  T4           3            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"
               vv
clus             N0  N1 N2+N3
  TTK MUTATED    12   1     5
  TTK WILD-TYPE 295  88    67
D381V5, multiclass
       clus
vv      TTK MUTATED TTK WILD-TYPE
  N0             12           295
  N1              1            88
  N2+N3           5            67
[1] 3 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
  TTK MUTATED    15   1
  TTK WILD-TYPE 312  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED     15    1
  TTK WILD-TYPE  312   22
   clus
vv  TTK MUTATED TTK WILD-TYPE
  0          15           312
  1           1            22
[1] 2 2
[1] FALSE
D381V7, binary
               cls
clus              0   1
  TTK MUTATED     9   9
  TTK WILD-TYPE 250 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      9    9
  TTK WILD-TYPE  250  212
        clus
vv       TTK MUTATED TTK WILD-TYPE
  FEMALE           9           250
  MALE             9           212
[1] 2 2
[1] FALSE
D381V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TTK MUTATED                            1                                 4
  TTK WILD-TYPE                         17                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TTK MUTATED                                                   12
  TTK WILD-TYPE                                                282
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TTK MUTATED                                            0
  TTK WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TTK MUTATED                                               1
  TTK WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  TTK MUTATED                                0
  TTK WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  TTK MUTATED                                    0                            0
  TTK WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  TTK MUTATED                               0
  TTK WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TTK MUTATED                                               0
  TTK WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  TTK MUTATED                              0
  TTK WILD-TYPE                            9
D381V9, multiclass
                                                    clus
vv                                                   TTK MUTATED TTK WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          12           282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V10, binary
               cls
clus              0   1
  TTK MUTATED     1  17
  TTK WILD-TYPE  19 443
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      1   17
  TTK WILD-TYPE   19  443
     clus
vv    TTK MUTATED TTK WILD-TYPE
  NO            1            19
  YES          17           443
[1] 2 2
[1] FALSE
D381V11, continuous
D381V12, continuous
               vv
clus             R0  R1  R2  RX
  TTK MUTATED    12   1   0   0
  TTK WILD-TYPE 298  10   4  25
D381V13, multiclass
    clus
vv   TTK MUTATED TTK WILD-TYPE
  R0          12           298
  R1           1            10
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTK MUTATED                                  0     0
  TTK WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TTK MUTATED                           2    13
  TTK WILD-TYPE                        27   364
D381V14, multiclass
                                  clus
vv                                 TTK MUTATED TTK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  2            27
  WHITE                                     13           364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V15, binary
               cls
clus              0   1
  TTK MUTATED     0  14
  TTK WILD-TYPE   6 335
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      0   14
  TTK WILD-TYPE    6  335
                        clus
vv                       TTK MUTATED TTK WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          14           335
[1] 2 2
[1] FALSE

Clustering(382) Variable = GGNBP2 MUTATION ANALYSIS
D382V1, survival
                  sevent
clus2                0   1
  GGNBP2 MUTATED     9   2
  GGNBP2 WILD-TYPE 306 139
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              11              445 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
               2              139 
$`GGNBP2 MUTATED`
TCGA-05-4424 TCGA-44-3398 TCGA-44-6147 TCGA-49-6744 TCGA-49-6761 TCGA-50-6590 
       30.02        38.24        27.78        29.26        11.64        42.35 
TCGA-55-8089 TCGA-55-8507 TCGA-69-7980 TCGA-91-6829 TCGA-93-8067 
        3.29         0.26        12.56        41.36         6.12 

$`GGNBP2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
       28.37        12.59        23.77        10.78         9.93        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 
       55.89        14.63        12.13        17.16        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.30         2.93        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         0.10        52.60        23.38        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        0.20        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
            0.26             0.00 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
           42.35           223.96 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
           27.78            17.98 
[1] "0.3 - 42.4 (27.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.6"
D382V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GGNBP2 MUTATED         1        4        3         1         1          1
  GGNBP2 WILD-TYPE       3      119      130        45        66         69
                  vv
clus               STAGE IIIB STAGE IV
  GGNBP2 MUTATED            0        0
  GGNBP2 WILD-TYPE         11       25
D382V3, multiclass
            clus
vv           GGNBP2 MUTATED GGNBP2 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                4              119
  STAGE IB                3              130
  STAGE IIA               1               45
  STAGE IIB               1               66
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GGNBP2 MUTATED     6   4   1   0
  GGNBP2 WILD-TYPE 149 257  42  18
D382V4, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  T1              6              149
  T2              4              257
  T3              1               42
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  GGNBP2 MUTATED     8   1     1
  GGNBP2 WILD-TYPE 299  88    71
D382V5, multiclass
       clus
vv      GGNBP2 MUTATED GGNBP2 WILD-TYPE
  N0                 8              299
  N1                 1               88
  N2+N3              1               71
[1] 3 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
  GGNBP2 MUTATED     6   0
  GGNBP2 WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      6    0
  GGNBP2 WILD-TYPE  321   23
   clus
vv  GGNBP2 MUTATED GGNBP2 WILD-TYPE
  0              6              321
  1              0               23
[1] 2 2
[1] FALSE
D382V7, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     6   5
  GGNBP2 WILD-TYPE 253 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      6    5
  GGNBP2 WILD-TYPE  253  216
        clus
vv       GGNBP2 MUTATED GGNBP2 WILD-TYPE
  FEMALE              6              253
  MALE                5              216
[1] 2 2
[1] FALSE
D382V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GGNBP2 MUTATED                            0                                 2
  GGNBP2 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GGNBP2 MUTATED                                                    8
  GGNBP2 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GGNBP2 MUTATED                                            0
  GGNBP2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GGNBP2 MUTATED                                               1
  GGNBP2 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  GGNBP2 MUTATED                                0
  GGNBP2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  GGNBP2 MUTATED                                    0
  GGNBP2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GGNBP2 MUTATED                              0                             0
  GGNBP2 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GGNBP2 MUTATED                                               0
  GGNBP2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  GGNBP2 MUTATED                              0
  GGNBP2 WILD-TYPE                            9
D382V9, multiclass
                                                    clus
vv                                                   GGNBP2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   GGNBP2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V10, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     0  11
  GGNBP2 WILD-TYPE  20 449
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      0   11
  GGNBP2 WILD-TYPE   20  449
     clus
vv    GGNBP2 MUTATED GGNBP2 WILD-TYPE
  NO               0               20
  YES             11              449
[1] 2 2
[1] FALSE
D382V11, continuous
D382V12, continuous
                  vv
clus                R0  R1  R2  RX
  GGNBP2 MUTATED     6   1   0   1
  GGNBP2 WILD-TYPE 304  10   4  24
D382V13, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  R0              6              304
  R1              1               10
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGNBP2 MUTATED                                  0     1
  GGNBP2 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GGNBP2 MUTATED                           0     9
  GGNBP2 WILD-TYPE                        29   368
D382V14, multiclass
                                  clus
vv                                 GGNBP2 MUTATED GGNBP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V15, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     0   9
  GGNBP2 WILD-TYPE   6 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      0    9
  GGNBP2 WILD-TYPE    6  340
                        clus
vv                       GGNBP2 MUTATED GGNBP2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              9              340
[1] 2 2
[1] FALSE

Clustering(383) Variable = ADAM23 MUTATION ANALYSIS
D383V1, survival
                  sevent
clus2                0   1
  ADAM23 MUTATED    18   8
  ADAM23 WILD-TYPE 297 133
  ADAM23 MUTATED ADAM23 WILD-TYPE 
              26              430 
  ADAM23 MUTATED ADAM23 WILD-TYPE 
               8              133 
$`ADAM23 MUTATED`
TCGA-05-4249 TCGA-05-5425 TCGA-44-5643 TCGA-44-5644 TCGA-44-6774 TCGA-44-7662 
       50.07        29.00        33.30        28.37        21.63         7.17 
TCGA-44-7670 TCGA-44-8120 TCGA-49-4487 TCGA-49-6743 TCGA-49-6767 TCGA-50-5930 
       29.00         8.55        28.11        12.13        22.26         9.27 
TCGA-50-5931 TCGA-50-6593 TCGA-55-6968 TCGA-55-6979 TCGA-55-8094 TCGA-55-8208 
       14.27        11.05        42.51         7.79         0.13        22.16 
TCGA-55-A4DG TCGA-69-7974 TCGA-78-8662 TCGA-86-8073 TCGA-97-7547 TCGA-97-A4M7 
       19.99         6.05       110.50        24.33        64.60        20.68 
TCGA-99-8025 TCGA-MP-A4TI 
       34.85        14.10 

$`ADAM23 WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06         6.25        26.56        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
       23.77        10.78         9.93        27.78        23.15        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       12.03        36.07        18.87        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       55.89        14.63        29.26        17.16        11.64        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        8.22        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        15.81        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      214.62        39.75        77.59        10.55        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        16.70        24.49         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       15.75        16.08        15.65        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       20.52        17.75        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        2.43        10.09        29.46        11.05        14.66        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ADAM23 MUTATED ADAM23 WILD-TYPE 
            0.13             0.00 
  ADAM23 MUTATED ADAM23 WILD-TYPE 
          110.50           223.96 
  ADAM23 MUTATED ADAM23 WILD-TYPE 
          21.895           17.735 
[1] "0.1 - 110.5 (21.9)" "0.0 - 224.0 (17.7)"
[1] "hr=" "1.2"
D383V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADAM23 MUTATED         0        4        8         2         3          8
  ADAM23 WILD-TYPE       4      119      125        44        64         62
                  vv
clus               STAGE IIIB STAGE IV
  ADAM23 MUTATED            0        2
  ADAM23 WILD-TYPE         11       23
D383V3, multiclass
            clus
vv           ADAM23 MUTATED ADAM23 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                8              125
  STAGE IIA               2               44
  STAGE IIB               3               64
  STAGE IIIA              8               62
  STAGE IIIB              0               11
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM23 MUTATED     9  16   2   0
  ADAM23 WILD-TYPE 146 245  41  18
D383V4, multiclass
    clus
vv   ADAM23 MUTATED ADAM23 WILD-TYPE
  T1              9              146
  T2             16              245
  T3              2               41
  T4              0               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"
                  vv
clus                N0  N1 N2+N3
  ADAM23 MUTATED    15   4     8
  ADAM23 WILD-TYPE 292  85    64
D383V5, multiclass
       clus
vv      ADAM23 MUTATED ADAM23 WILD-TYPE
  N0                15              292
  N1                 4               85
  N2+N3              8               64
[1] 3 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
  ADAM23 MUTATED    18   2
  ADAM23 WILD-TYPE 309  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM23 MUTATED     18    2
  ADAM23 WILD-TYPE  309   21
   clus
vv  ADAM23 MUTATED ADAM23 WILD-TYPE
  0             18              309
  1              2               21
[1] 2 2
[1] FALSE
D383V7, binary
                  cls
clus                 0   1
  ADAM23 MUTATED    15  12
  ADAM23 WILD-TYPE 244 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM23 MUTATED     15   12
  ADAM23 WILD-TYPE  244  209
        clus
vv       ADAM23 MUTATED ADAM23 WILD-TYPE
  FEMALE             15              244
  MALE               12              209
[1] 2 2
[1] FALSE
D383V8, continuous
[1] "Remove cluster labels:" "ADAM23 MUTATED"        
clus
  ADAM23 MUTATED ADAM23 WILD-TYPE 
               2               82 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-53-A4EZ 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5778 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-73-4662       TCGA-73-4666       TCGA-73-4668       TCGA-73-4676 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A4JF 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7348       TCGA-93-8067 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-99-7458       TCGA-MN-A4N1 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5 
"ADAM23 WILD-TYPE" "ADAM23 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADAM23 MUTATED                            0                                 5
  ADAM23 WILD-TYPE                         18                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADAM23 MUTATED                                                   19
  ADAM23 WILD-TYPE                                                275
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADAM23 MUTATED                                            0
  ADAM23 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADAM23 MUTATED                                               1
  ADAM23 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ADAM23 MUTATED                                1
  ADAM23 WILD-TYPE                              1
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ADAM23 MUTATED                                    0
  ADAM23 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADAM23 MUTATED                              0                             1
  ADAM23 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADAM23 MUTATED                                               0
  ADAM23 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ADAM23 MUTATED                              0
  ADAM23 WILD-TYPE                            9
D383V9, multiclass
                                                    clus
vv                                                   ADAM23 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ADAM23 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              275
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V10, binary
                  cls
clus                 0   1
  ADAM23 MUTATED     4  23
  ADAM23 WILD-TYPE  16 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM23 MUTATED      4   23
  ADAM23 WILD-TYPE   16  437
     clus
vv    ADAM23 MUTATED ADAM23 WILD-TYPE
  NO               4               16
  YES             23              437
[1] 2 2
[1] FALSE
D383V11, continuous
D383V12, continuous
                  vv
clus                R0  R1  R2  RX
  ADAM23 MUTATED    15   0   0   0
  ADAM23 WILD-TYPE 295  11   4  25
D383V13, multiclass
    clus
vv   ADAM23 MUTATED ADAM23 WILD-TYPE
  R0             15              295
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM23 MUTATED                                  0     0
  ADAM23 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM23 MUTATED                           3    20
  ADAM23 WILD-TYPE                        26   357
D383V14, multiclass
                                  clus
vv                                 ADAM23 MUTATED ADAM23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     3               26
  WHITE                                        20              357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V15, binary
                  cls
clus                 0   1
  ADAM23 MUTATED     1  19
  ADAM23 WILD-TYPE   5 330
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM23 MUTATED      1   19
  ADAM23 WILD-TYPE    5  330
                        clus
vv                       ADAM23 MUTATED ADAM23 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             19              330
[1] 2 2
[1] FALSE

Clustering(384) Variable = CHD8 MUTATION ANALYSIS
D384V1, survival
                sevent
clus2              0   1
  CHD8 MUTATED    15   8
  CHD8 WILD-TYPE 300 133
  CHD8 MUTATED CHD8 WILD-TYPE 
            23            433 
  CHD8 MUTATED CHD8 WILD-TYPE 
             8            133 
$`CHD8 MUTATED`
TCGA-44-2657 TCGA-44-5643 TCGA-44-6777 TCGA-49-6745 TCGA-50-5072 TCGA-55-1595 
       13.15        33.30        32.45        17.16         8.22        48.62 
TCGA-55-6968 TCGA-55-7283 TCGA-55-8205 TCGA-55-8506 TCGA-62-8394 TCGA-67-3771 
       42.51         1.15         1.08         0.36         4.57        20.05 
TCGA-69-7979 TCGA-73-4659 TCGA-78-7155 TCGA-78-7633 TCGA-86-8054 TCGA-93-7347 
        2.93        23.38        38.50        32.68        24.49         9.76 
TCGA-95-A4VN TCGA-97-A4M5 TCGA-MP-A4T4 TCGA-MP-A4TI TCGA-NJ-A4YQ 
       18.18        20.84        86.04        14.10        29.13 

$`CHD8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 
       44.61        14.73        26.30         4.37        46.98        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        63.72        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 
       55.89        14.63        12.13        29.26        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 
       34.29        30.54        13.94         9.21        23.05         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
        0.07        32.65         0.79        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1.74         0.59         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       19.99        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 
        4.24         7.04         2.01         0.10        52.60        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        10.75        39.35        10.55       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       16.70         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.18         1.45        19.82         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
        2.76        86.14        58.45        49.35        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        14.66        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CHD8 MUTATED CHD8 WILD-TYPE 
          0.36           0.00 
  CHD8 MUTATED CHD8 WILD-TYPE 
         86.04         223.96 
  CHD8 MUTATED CHD8 WILD-TYPE 
         20.05          17.92 
[1] "0.4 - 86.0 (20.1)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.2"
D384V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CHD8 MUTATED         0        6        4         2         4          6
  CHD8 WILD-TYPE       4      117      129        44        63         64
                vv
clus             STAGE IIIB STAGE IV
  CHD8 MUTATED            1        1
  CHD8 WILD-TYPE         10       24
D384V3, multiclass
            clus
vv           CHD8 MUTATED CHD8 WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              4            129
  STAGE IIA             2             44
  STAGE IIB             4             63
  STAGE IIIA            6             64
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD8 MUTATED     6  14   3   1
  CHD8 WILD-TYPE 149 247  40  17
D384V4, multiclass
    clus
vv   CHD8 MUTATED CHD8 WILD-TYPE
  T1            6            149
  T2           14            247
  T3            3             40
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  CHD8 MUTATED    11   4     7
  CHD8 WILD-TYPE 296  85    65
D384V5, multiclass
       clus
vv      CHD8 MUTATED CHD8 WILD-TYPE
  N0              11            296
  N1               4             85
  N2+N3            7             65
[1] 3 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
  CHD8 MUTATED    18   1
  CHD8 WILD-TYPE 309  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED     18    1
  CHD8 WILD-TYPE  309   22
   clus
vv  CHD8 MUTATED CHD8 WILD-TYPE
  0           18            309
  1            1             22
[1] 2 2
[1] FALSE
D384V7, binary
                cls
clus               0   1
  CHD8 MUTATED    14  10
  CHD8 WILD-TYPE 245 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED     14   10
  CHD8 WILD-TYPE  245  211
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  FEMALE           14            245
  MALE             10            211
[1] 2 2
[1] FALSE
D384V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHD8 MUTATED                            2                                 4
  CHD8 WILD-TYPE                         16                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHD8 MUTATED                                                   14
  CHD8 WILD-TYPE                                                280
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CHD8 MUTATED                                            0
  CHD8 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CHD8 MUTATED                                               1
  CHD8 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  CHD8 MUTATED                                1
  CHD8 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  CHD8 MUTATED                                    0
  CHD8 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CHD8 MUTATED                              0                             1
  CHD8 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CHD8 MUTATED                                               1
  CHD8 WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  CHD8 MUTATED                              0
  CHD8 WILD-TYPE                            9
D384V9, multiclass
                                                    clus
vv                                                   CHD8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           14
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   CHD8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V10, binary
                cls
clus               0   1
  CHD8 MUTATED     3  21
  CHD8 WILD-TYPE  17 439
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      3   21
  CHD8 WILD-TYPE   17  439
     clus
vv    CHD8 MUTATED CHD8 WILD-TYPE
  NO             3             17
  YES           21            439
[1] 2 2
[1] FALSE
D384V11, continuous
D384V12, continuous
                vv
clus              R0  R1  R2  RX
  CHD8 MUTATED    13   0   1   1
  CHD8 WILD-TYPE 297  11   3  24
D384V13, multiclass
    clus
vv   CHD8 MUTATED CHD8 WILD-TYPE
  R0           13            297
  R1            0             11
  R2            1              3
  RX            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD8 MUTATED                                  0     1
  CHD8 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD8 MUTATED                           2    20
  CHD8 WILD-TYPE                        27   357
D384V14, multiclass
                                  clus
vv                                 CHD8 MUTATED CHD8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   2             27
  WHITE                                      20            357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V15, binary
                cls
clus               0   1
  CHD8 MUTATED     0  18
  CHD8 WILD-TYPE   6 331
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      0   18
  CHD8 WILD-TYPE    6  331
                        clus
vv                       CHD8 MUTATED CHD8 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           18            331
[1] 2 2
[1] FALSE

Clustering(385) Variable = TBC1D14 MUTATION ANALYSIS
D385V1, survival
                   sevent
clus2                 0   1
  TBC1D14 MUTATED     5   2
  TBC1D14 WILD-TYPE 310 139
  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
                7               449 
  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
                2               139 
$`TBC1D14 MUTATED`
TCGA-64-5779 TCGA-69-7980 TCGA-86-8073 TCGA-86-8278 TCGA-95-7562 TCGA-J2-8192 
       28.41        12.56        24.33        15.65         2.86        24.30 
TCGA-MP-A4T8 
        5.29 

$`TBC1D14 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98         2.04        42.90        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30         2.93        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        15.75        16.08        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.22        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85        36.76         1.45         5.59        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        86.04        58.85         5.49        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
             2.86              0.00 
  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
            28.41            223.96 
  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
            15.65             18.08 
[1] "2.9 - 28.4 (15.7)"  "0.0 - 224.0 (18.1)"
[1] "hr=" "1.6"
D385V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TBC1D14 MUTATED         1        0        2         2         1          2
  TBC1D14 WILD-TYPE       3      123      131        44        66         68
                   vv
clus                STAGE IIIB STAGE IV
  TBC1D14 MUTATED            0        0
  TBC1D14 WILD-TYPE         11       25
D385V3, multiclass
            clus
vv           TBC1D14 MUTATED TBC1D14 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0               123
  STAGE IB                 2               131
  STAGE IIA                2                44
  STAGE IIB                1                66
  STAGE IIIA               2                68
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBC1D14 MUTATED     1   7   0   0
  TBC1D14 WILD-TYPE 154 254  43  18
D385V4, multiclass
    clus
vv   TBC1D14 MUTATED TBC1D14 WILD-TYPE
  T1               1               154
  T2               7               254
  T3               0                43
  T4               0                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"
                   vv
clus                 N0  N1 N2+N3
  TBC1D14 MUTATED     3   3     2
  TBC1D14 WILD-TYPE 304  86    70
D385V5, multiclass
       clus
vv      TBC1D14 MUTATED TBC1D14 WILD-TYPE
  N0                  3               304
  N1                  3                86
  N2+N3               2                70
[1] 3 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
  TBC1D14 MUTATED     7   0
  TBC1D14 WILD-TYPE 320  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D14 MUTATED      7    0
  TBC1D14 WILD-TYPE  320   23
   clus
vv  TBC1D14 MUTATED TBC1D14 WILD-TYPE
  0               7               320
  1               0                23
[1] 2 2
[1] FALSE
D385V7, binary
                   cls
clus                  0   1
  TBC1D14 MUTATED     3   5
  TBC1D14 WILD-TYPE 256 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D14 MUTATED      3    5
  TBC1D14 WILD-TYPE  256  216
        clus
vv       TBC1D14 MUTATED TBC1D14 WILD-TYPE
  FEMALE               3               256
  MALE                 5               216
[1] 2 2
[1] FALSE
D385V8, continuous
[1] "Remove cluster labels:" "TBC1D14 MUTATED"       
clus
  TBC1D14 MUTATED TBC1D14 WILD-TYPE 
                1                83 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-53-A4EZ 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-A48Z 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-55-A490        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-73-7498        TCGA-73-7499 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-75-5122        TCGA-83-5908        TCGA-86-7701        TCGA-86-7711 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7954        TCGA-86-7955 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-86-8055        TCGA-86-8056        TCGA-86-8074        TCGA-86-8075 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8279        TCGA-86-8281        TCGA-86-8358 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6849        TCGA-93-7348 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-99-7458 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" "TBC1D14 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  TBC1D14 MUTATED                            1
  TBC1D14 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  TBC1D14 MUTATED                                   0
  TBC1D14 WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TBC1D14 MUTATED                                                    6
  TBC1D14 WILD-TYPE                                                288
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TBC1D14 MUTATED                                            0
  TBC1D14 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TBC1D14 MUTATED                                               1
  TBC1D14 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  TBC1D14 MUTATED                                0
  TBC1D14 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  TBC1D14 MUTATED                                    0
  TBC1D14 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TBC1D14 MUTATED                              0                             0
  TBC1D14 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TBC1D14 MUTATED                                               0
  TBC1D14 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  TBC1D14 MUTATED                              0
  TBC1D14 WILD-TYPE                            9
D385V9, multiclass
                                                    clus
vv                                                   TBC1D14 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   TBC1D14 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V10, binary
                   cls
clus                  0   1
  TBC1D14 MUTATED     1   7
  TBC1D14 WILD-TYPE  19 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D14 MUTATED      1    7
  TBC1D14 WILD-TYPE   19  453
     clus
vv    TBC1D14 MUTATED TBC1D14 WILD-TYPE
  NO                1                19
  YES               7               453
[1] 2 2
[1] FALSE
D385V11, continuous
D385V12, continuous
                   vv
clus                 R0  R1  R2  RX
  TBC1D14 MUTATED     5   0   0   1
  TBC1D14 WILD-TYPE 305  11   4  24
D385V13, multiclass
    clus
vv   TBC1D14 MUTATED TBC1D14 WILD-TYPE
  R0               5               305
  R1               0                11
  R2               0                 4
  RX               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBC1D14 MUTATED                                  0     0
  TBC1D14 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TBC1D14 MUTATED                           1     5
  TBC1D14 WILD-TYPE                        28   372
D385V14, multiclass
                                  clus
vv                                 TBC1D14 MUTATED TBC1D14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                          5               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V15, binary
                   cls
clus                  0   1
  TBC1D14 MUTATED     0   6
  TBC1D14 WILD-TYPE   6 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D14 MUTATED      0    6
  TBC1D14 WILD-TYPE    6  343
                        clus
vv                       TBC1D14 MUTATED TBC1D14 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               6               343
[1] 2 2
[1] FALSE

Clustering(386) Variable = GPR128 MUTATION ANALYSIS
D386V1, survival
                  sevent
clus2                0   1
  GPR128 MUTATED    11   5
  GPR128 WILD-TYPE 304 136
  GPR128 MUTATED GPR128 WILD-TYPE 
              16              440 
  GPR128 MUTATED GPR128 WILD-TYPE 
               5              136 
$`GPR128 MUTATED`
TCGA-05-4396 TCGA-44-4112 TCGA-44-7660 TCGA-50-5049 TCGA-50-6594 TCGA-55-7903 
        9.96        26.56        19.46        70.55        12.16        18.64 
TCGA-62-A46O TCGA-64-5815 TCGA-78-7536 TCGA-86-6851 TCGA-86-8073 TCGA-91-6830 
       47.80        28.47         8.02         5.88        24.33         1.97 
TCGA-93-8067 TCGA-97-7937 TCGA-97-A4M3 TCGA-MN-A4N4 
        6.12         5.95        17.75        38.63 

$`GPR128 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 
       42.77        37.15        38.24        34.06         6.25        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        14.60        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        14.63        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        71.47        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       22.55        42.35         3.91        25.55        11.05         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94         9.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 
        1.28         1.12         0.79         1.78         1.45         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 
       87.98         2.04        42.90        28.41        51.25        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31         1.32         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        13.87        20.55        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       16.70        24.49         4.08         4.57         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       16.08        15.65        15.85        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       25.48         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 
       20.19        21.44        19.76        20.52        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81         0.20        27.19         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  GPR128 MUTATED GPR128 WILD-TYPE 
            1.97             0.00 
  GPR128 MUTATED GPR128 WILD-TYPE 
           70.55           223.96 
  GPR128 MUTATED GPR128 WILD-TYPE 
          18.195           18.030 
[1] "2.0 - 70.5 (18.2)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.1"
D386V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GPR128 MUTATED         0        5        6         2         1          2
  GPR128 WILD-TYPE       4      118      127        44        66         68
                  vv
clus               STAGE IIIB STAGE IV
  GPR128 MUTATED            1        0
  GPR128 WILD-TYPE         10       25
D386V3, multiclass
            clus
vv           GPR128 MUTATED GPR128 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              118
  STAGE IB                6              127
  STAGE IIA               2               44
  STAGE IIB               1               66
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR128 MUTATED     6   9   1   1
  GPR128 WILD-TYPE 149 252  42  17
D386V4, multiclass
    clus
vv   GPR128 MUTATED GPR128 WILD-TYPE
  T1              6              149
  T2              9              252
  T3              1               42
  T4              1               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"
                  vv
clus                N0  N1 N2+N3
  GPR128 MUTATED    11   4     2
  GPR128 WILD-TYPE 296  85    70
D386V5, multiclass
       clus
vv      GPR128 MUTATED GPR128 WILD-TYPE
  N0                11              296
  N1                 4               85
  N2+N3              2               70
[1] 3 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
  GPR128 MUTATED    12   0
  GPR128 WILD-TYPE 315  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED     12    0
  GPR128 WILD-TYPE  315   23
   clus
vv  GPR128 MUTATED GPR128 WILD-TYPE
  0             12              315
  1              0               23
[1] 2 2
[1] FALSE
D386V7, binary
                  cls
clus                 0   1
  GPR128 MUTATED     7  10
  GPR128 WILD-TYPE 252 211
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      7   10
  GPR128 WILD-TYPE  252  211
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  FEMALE              7              252
  MALE               10              211
[1] 2 2
[1] FALSE
D386V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GPR128 MUTATED                            0                                 4
  GPR128 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GPR128 MUTATED                                                   11
  GPR128 WILD-TYPE                                                283
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GPR128 MUTATED                                            0
  GPR128 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GPR128 MUTATED                                               1
  GPR128 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  GPR128 MUTATED                                0
  GPR128 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  GPR128 MUTATED                                    1
  GPR128 WILD-TYPE                                  2
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GPR128 MUTATED                              0                             0
  GPR128 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GPR128 MUTATED                                               0
  GPR128 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  GPR128 MUTATED                              0
  GPR128 WILD-TYPE                            9
D386V9, multiclass
                                                    clus
vv                                                   GPR128 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              1
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   GPR128 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V10, binary
                  cls
clus                 0   1
  GPR128 MUTATED     2  15
  GPR128 WILD-TYPE  18 445
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      2   15
  GPR128 WILD-TYPE   18  445
     clus
vv    GPR128 MUTATED GPR128 WILD-TYPE
  NO               2               18
  YES             15              445
[1] 2 2
[1] FALSE
D386V11, continuous
D386V12, continuous
                  vv
clus                R0  R1  R2  RX
  GPR128 MUTATED     9   0   0   1
  GPR128 WILD-TYPE 301  11   4  24
D386V13, multiclass
    clus
vv   GPR128 MUTATED GPR128 WILD-TYPE
  R0              9              301
  R1              0               11
  R2              0                4
  RX              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR128 MUTATED                                  0     1
  GPR128 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR128 MUTATED                           1    13
  GPR128 WILD-TYPE                        28   364
D386V14, multiclass
                                  clus
vv                                 GPR128 MUTATED GPR128 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        13              364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V15, binary
                  cls
clus                 0   1
  GPR128 MUTATED     0  14
  GPR128 WILD-TYPE   6 335
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      0   14
  GPR128 WILD-TYPE    6  335
                        clus
vv                       GPR128 MUTATED GPR128 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             14              335
[1] 2 2
[1] FALSE

Clustering(387) Variable = RPL6 MUTATION ANALYSIS
D387V1, survival
                sevent
clus2              0   1
  RPL6 MUTATED     1   2
  RPL6 WILD-TYPE 314 139
  RPL6 MUTATED RPL6 WILD-TYPE 
             3            453 
  RPL6 MUTATED RPL6 WILD-TYPE 
             2            139 
$`RPL6 MUTATED`
TCGA-50-5944 TCGA-78-7145 TCGA-MP-A4T7 
       25.12        27.16         5.49 

$`RPL6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       15.12        18.64        29.03        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        18.84        14.04         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
        1.25        39.09        23.51       163.10         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58        35.93        21.90        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29         1.12         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  RPL6 MUTATED RPL6 WILD-TYPE 
          5.49           0.00 
  RPL6 MUTATED RPL6 WILD-TYPE 
         27.16         223.96 
  RPL6 MUTATED RPL6 WILD-TYPE 
         25.12          17.98 
[1] "5.5 - 27.2 (25.1)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "3"  
D387V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RPL6 MUTATED         0        1        0         0         0          0
  RPL6 WILD-TYPE       4      122      133        46        67         70
                vv
clus             STAGE IIIB STAGE IV
  RPL6 MUTATED            0        2
  RPL6 WILD-TYPE         11       23
D387V3, multiclass
            clus
vv           RPL6 MUTATED RPL6 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              0            133
  STAGE IIA             0             46
  STAGE IIB             0             67
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPL6 MUTATED     1   1   0   1
  RPL6 WILD-TYPE 154 260  43  17
D387V4, multiclass
    clus
vv   RPL6 MUTATED RPL6 WILD-TYPE
  T1            1            154
  T2            1            260
  T3            0             43
  T4            1             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"
                vv
clus              N0  N1 N2+N3
  RPL6 MUTATED     2   1     0
  RPL6 WILD-TYPE 305  88    72
D387V5, multiclass
       clus
vv      RPL6 MUTATED RPL6 WILD-TYPE
  N0               2            305
  N1               1             88
  N2+N3            0             72
[1] 3 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
  RPL6 MUTATED     1   2
  RPL6 WILD-TYPE 326  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL6 MUTATED      1    2
  RPL6 WILD-TYPE  326   21
   clus
vv  RPL6 MUTATED RPL6 WILD-TYPE
  0            1            326
  1            2             21
[1] 2 2
[1] FALSE
D387V7, binary
                cls
clus               0   1
  RPL6 MUTATED     3   0
  RPL6 WILD-TYPE 256 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL6 MUTATED      3    0
  RPL6 WILD-TYPE  256  221
        clus
vv       RPL6 MUTATED RPL6 WILD-TYPE
  FEMALE            3            256
  MALE              0            221
[1] 2 2
[1] FALSE
D387V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RPL6 MUTATED                            1                                 0
  RPL6 WILD-TYPE                         17                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RPL6 MUTATED                                                    2
  RPL6 WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RPL6 MUTATED                                            0
  RPL6 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RPL6 MUTATED                                               0
  RPL6 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RPL6 MUTATED                                0
  RPL6 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RPL6 MUTATED                                    0
  RPL6 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RPL6 MUTATED                              0                             0
  RPL6 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RPL6 MUTATED                                               0
  RPL6 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RPL6 MUTATED                              0
  RPL6 WILD-TYPE                            9
D387V9, multiclass
                                                    clus
vv                                                   RPL6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RPL6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V10, binary
                cls
clus               0   1
  RPL6 MUTATED     0   3
  RPL6 WILD-TYPE  20 457
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL6 MUTATED      0    3
  RPL6 WILD-TYPE   20  457
     clus
vv    RPL6 MUTATED RPL6 WILD-TYPE
  NO             0             20
  YES            3            457
[1] 2 2
[1] FALSE
D387V11, continuous
[1] "Remove cluster labels:" "RPL6 MUTATED"          
clus
  RPL6 MUTATED RPL6 WILD-TYPE 
             2            331 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4396 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4397     TCGA-05-4398     TCGA-05-4405     TCGA-05-4410 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4415     TCGA-05-4417     TCGA-05-4418     TCGA-05-4420 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4422     TCGA-05-4424     TCGA-05-4425     TCGA-05-4426 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4430     TCGA-05-4432     TCGA-05-4433 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4434     TCGA-05-5420     TCGA-05-5423     TCGA-05-5425 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-5428     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-4629     TCGA-38-4631 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-38-4632     TCGA-38-7271     TCGA-38-A44F     TCGA-44-2656 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-2657     TCGA-44-3396     TCGA-44-3398     TCGA-44-3918 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-4112     TCGA-44-5643     TCGA-44-5644     TCGA-44-5645 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6146     TCGA-44-6148 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4490     TCGA-49-4494 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4507     TCGA-49-4510 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-4514     TCGA-49-6742     TCGA-49-6743     TCGA-49-6744 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-6745     TCGA-49-6761     TCGA-49-6767     TCGA-50-5051 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-5072     TCGA-50-5931     TCGA-50-5939     TCGA-50-5941 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-5942     TCGA-50-6590     TCGA-50-7109     TCGA-50-8457 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-8459     TCGA-53-7624     TCGA-53-7626     TCGA-53-7813 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-53-A4EZ     TCGA-55-6543     TCGA-55-6971     TCGA-55-6983 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-6985     TCGA-55-7281     TCGA-55-7283     TCGA-55-7574 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7724     TCGA-55-7725     TCGA-55-7726     TCGA-55-7728 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7903     TCGA-55-7907     TCGA-55-7910     TCGA-55-7911 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-7994     TCGA-55-7995     TCGA-55-8089 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8203     TCGA-55-8205     TCGA-55-8208     TCGA-55-8299 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8301     TCGA-55-8302     TCGA-55-8507     TCGA-55-8511 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8514     TCGA-55-8614     TCGA-55-8615 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-A46O     TCGA-62-A46P 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A470     TCGA-62-A471 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1676     TCGA-64-1677     TCGA-64-1679 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-64-5781     TCGA-64-5815     TCGA-69-7761     TCGA-69-7763 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-7764     TCGA-69-7973     TCGA-69-7974     TCGA-69-7978 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-7979     TCGA-69-7980     TCGA-69-8253     TCGA-69-8254 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-8255     TCGA-69-A59K     TCGA-73-4658     TCGA-73-4659 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-7498     TCGA-75-5122 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-75-5125     TCGA-75-5126     TCGA-75-6203     TCGA-75-6206 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-75-6207     TCGA-75-6211     TCGA-75-6214     TCGA-75-7027 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7146     TCGA-78-7147     TCGA-78-7148 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7149     TCGA-78-7150     TCGA-78-7152     TCGA-78-7153 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7154     TCGA-78-7155     TCGA-78-7156     TCGA-78-7158 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7159     TCGA-78-7160     TCGA-78-7161     TCGA-78-7162 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7163     TCGA-78-7166     TCGA-78-7167     TCGA-78-7220 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7535     TCGA-78-7536     TCGA-78-7537     TCGA-78-7539 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-80-5608     TCGA-80-5611     TCGA-83-5908     TCGA-86-6851 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7714     TCGA-86-7954 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8673     TCGA-86-8674     TCGA-91-6829 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-6830     TCGA-91-6835     TCGA-91-6836     TCGA-91-6840 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-6849     TCGA-91-7771     TCGA-91-8499     TCGA-91-A4BC 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-95-7039     TCGA-95-7043     TCGA-95-7562 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-95-7944     TCGA-95-7947     TCGA-95-7948     TCGA-95-A4VK 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546     TCGA-97-7547 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-7552     TCGA-97-7553     TCGA-97-7554     TCGA-97-7937 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-7938     TCGA-97-7941     TCGA-97-8171     TCGA-97-8172 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-8174     TCGA-97-8176     TCGA-97-8179     TCGA-97-A4LX 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2     TCGA-97-A4M3 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194     TCGA-J2-A4AD 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6     TCGA-L9-A443 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-L9-A444     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T8 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TD 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YF     TCGA-NJ-A4YG 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-NJ-A4YI     TCGA-NJ-A4YP     TCGA-NJ-A4YQ     TCGA-NJ-A55A 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-NJ-A55O     TCGA-NJ-A55R     TCGA-O1-A52J 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
D387V12, continuous
[1] "Remove cluster labels:" "RPL6 MUTATED"          
clus
  RPL6 MUTATED RPL6 WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     TCGA-44-3396 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-5644 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6147 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     TCGA-44-6776 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7661     TCGA-44-7662     TCGA-44-7667 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7670     TCGA-44-7672     TCGA-44-8117 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-1592     TCGA-55-1595     TCGA-55-5899     TCGA-55-6642 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-6712     TCGA-55-6971     TCGA-55-7227     TCGA-55-7283 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7728     TCGA-55-7907 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7914     TCGA-55-8089 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8615     TCGA-55-8620     TCGA-55-8621 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A493     TCGA-55-A494 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-8398     TCGA-64-1677     TCGA-64-1681     TCGA-64-5774 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-7761     TCGA-69-7763     TCGA-69-7764     TCGA-69-7765 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-7979     TCGA-69-8253     TCGA-69-8255 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-A59K     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4675     TCGA-73-4676 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-73-7498     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7146     TCGA-78-7147     TCGA-78-7148 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7149     TCGA-78-7150     TCGA-78-7152     TCGA-78-7153 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7154     TCGA-78-7155     TCGA-78-7156     TCGA-78-7158 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7159     TCGA-78-7160     TCGA-78-7161     TCGA-78-7162 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7163     TCGA-78-7166     TCGA-78-7167     TCGA-78-7220 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7535     TCGA-78-7536     TCGA-78-7537     TCGA-78-7539 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5607 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-80-5608     TCGA-83-5908     TCGA-86-6851     TCGA-86-7711 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-8054     TCGA-86-8055 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8281 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8669     TCGA-86-8673 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-91-6829     TCGA-91-6830 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-6836     TCGA-91-6840     TCGA-91-6849     TCGA-91-8499 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-A4BC     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7567     TCGA-95-7944     TCGA-95-7947 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-95-7948     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7553     TCGA-97-7554     TCGA-97-7941 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-8171     TCGA-97-8172     TCGA-97-8174     TCGA-97-8176 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-8179     TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-99-7458     TCGA-99-8025     TCGA-99-8028     TCGA-99-8032 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-J2-8194     TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-L4-A4E6     TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MN-A4N4     TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T8     TCGA-MP-A4T9 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  RPL6 MUTATED     2   1   0   0
  RPL6 WILD-TYPE 308  10   4  25
D387V13, multiclass
    clus
vv   RPL6 MUTATED RPL6 WILD-TYPE
  R0            2            308
  R1            1             10
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPL6 MUTATED                                  0     0
  RPL6 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPL6 MUTATED                           0     2
  RPL6 WILD-TYPE                        29   375
D387V14, multiclass
[1] "Remove cluster labels:" "RPL6 MUTATED"          
clus
  RPL6 MUTATED RPL6 WILD-TYPE 
             2            412 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-38-4625 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-38-4626     TCGA-38-4627     TCGA-38-4628     TCGA-38-4629 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-38-4630     TCGA-38-4631     TCGA-38-4632     TCGA-38-6178 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-38-7271     TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-2661     TCGA-44-2665     TCGA-44-3396     TCGA-44-3398 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-3919     TCGA-44-4112     TCGA-44-5643 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-5644     TCGA-44-5645     TCGA-44-6144     TCGA-44-6145 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6146     TCGA-44-6147     TCGA-44-6148     TCGA-44-6774 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-6776     TCGA-44-6777     TCGA-44-6778 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-6779     TCGA-44-7659     TCGA-44-7660     TCGA-44-7661 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-7662     TCGA-44-7667     TCGA-44-7669     TCGA-44-7670 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-7671     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4490 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4501     TCGA-49-4505     TCGA-49-4506 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-4507     TCGA-49-4510     TCGA-49-4512     TCGA-49-4514 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-49-6745 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-49-6761     TCGA-49-6767     TCGA-50-5044     TCGA-50-5045 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-5049     TCGA-50-5051     TCGA-50-5055     TCGA-50-5066 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-5068     TCGA-50-5072     TCGA-50-5930     TCGA-50-5931 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-5932     TCGA-50-5933     TCGA-50-5935     TCGA-50-5936 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-5939     TCGA-50-5941     TCGA-50-5942     TCGA-50-5946 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-6590     TCGA-50-6591     TCGA-50-6592     TCGA-50-6593 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-6594     TCGA-50-6595     TCGA-50-6597     TCGA-50-6673 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-50-7109     TCGA-50-8457     TCGA-50-8459     TCGA-50-8460 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-1592     TCGA-55-1595     TCGA-55-5899     TCGA-55-6543 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6712     TCGA-55-6968     TCGA-55-6969 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-6970     TCGA-55-6971     TCGA-55-6972     TCGA-55-6975 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-6978     TCGA-55-6979     TCGA-55-6980     TCGA-55-6981 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-6982     TCGA-55-6983     TCGA-55-6984     TCGA-55-6985 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-6986     TCGA-55-6987     TCGA-55-7227     TCGA-55-7281 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7284     TCGA-55-7570     TCGA-55-7573 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7727     TCGA-55-7816     TCGA-55-7903 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8085     TCGA-55-8087 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8090     TCGA-55-8091     TCGA-55-8092 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8203 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8204     TCGA-55-8205     TCGA-55-8206     TCGA-55-8207 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8505     TCGA-55-8506     TCGA-55-8507     TCGA-55-8508 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8510     TCGA-55-8511     TCGA-55-8512     TCGA-55-8513 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8614     TCGA-55-8615     TCGA-55-8616 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-55-A4DG     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1676     TCGA-64-1677     TCGA-64-1679 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5774     TCGA-64-5775     TCGA-64-5778 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-64-5779     TCGA-64-5781     TCGA-64-5815     TCGA-67-3771 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-67-3772     TCGA-67-3773     TCGA-67-4679     TCGA-67-6215 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-69-7760     TCGA-69-7761 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-7763     TCGA-69-7764     TCGA-69-7765     TCGA-69-7973 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-7978     TCGA-69-7979     TCGA-69-7980 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-69-8253     TCGA-69-8254     TCGA-69-8255     TCGA-69-A59K 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4658     TCGA-73-4659 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-73-7499     TCGA-78-7143     TCGA-78-7146     TCGA-78-7147 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7148     TCGA-78-7149     TCGA-78-7150     TCGA-78-7152 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7153     TCGA-78-7154     TCGA-78-7155     TCGA-78-7156 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7158     TCGA-78-7159     TCGA-78-7160     TCGA-78-7161 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7162     TCGA-78-7163     TCGA-78-7166     TCGA-78-7167 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7539 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-78-7540     TCGA-78-7542     TCGA-78-7633     TCGA-83-5908 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-6562     TCGA-86-6851     TCGA-86-7701     TCGA-86-7711 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8585     TCGA-86-8668 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-8672     TCGA-86-8673 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-86-A4P8     TCGA-91-6828     TCGA-91-6829     TCGA-91-6830 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-6831     TCGA-91-6835     TCGA-91-6836     TCGA-91-6840 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-6847     TCGA-91-6848     TCGA-91-6849     TCGA-91-7771 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-8496     TCGA-91-8497     TCGA-91-8499     TCGA-91-A4BC 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-95-7039     TCGA-95-7043     TCGA-95-7562     TCGA-95-7567 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-95-7944     TCGA-95-7947     TCGA-95-7948     TCGA-95-8039 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-95-8494     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7547     TCGA-97-7552     TCGA-97-7553 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-7554     TCGA-97-7937     TCGA-97-7938     TCGA-97-7941 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-8171     TCGA-97-8172     TCGA-97-8174     TCGA-97-8175 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-8176     TCGA-97-8177     TCGA-97-8179     TCGA-97-8552 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M6     TCGA-97-A4M7 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-99-7458     TCGA-99-8025     TCGA-99-8028     TCGA-99-8032 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-99-8033     TCGA-J2-8192     TCGA-J2-8194     TCGA-J2-A4AD 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SW     TCGA-MP-A4SY     TCGA-MP-A4T2 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T9     TCGA-MP-A4TA 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4TC     TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A5C7     TCGA-NJ-A4YF 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-NJ-A4YP     TCGA-NJ-A4YQ 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
    TCGA-NJ-A55A     TCGA-NJ-A55O     TCGA-NJ-A55R     TCGA-O1-A52J 
"RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" "RPL6 WILD-TYPE" 
D387V15, binary
                cls
clus               0   1
  RPL6 MUTATED     0   0
  RPL6 WILD-TYPE   6 349
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL6 MUTATED      0    0
  RPL6 WILD-TYPE    6  349

Clustering(388) Variable = FRZB MUTATION ANALYSIS
D388V1, survival
                sevent
clus2              0   1
  FRZB MUTATED     7   2
  FRZB WILD-TYPE 308 139
  FRZB MUTATED FRZB WILD-TYPE 
             9            447 
  FRZB MUTATED FRZB WILD-TYPE 
             2            139 
$`FRZB MUTATED`
TCGA-05-4427 TCGA-55-7995 TCGA-55-8511 TCGA-62-A46P TCGA-62-A46S TCGA-73-4668 
       26.01         0.16         0.30        19.53        54.35        15.35 
TCGA-86-8073 TCGA-95-A4VP TCGA-97-A4M0 
       24.33        19.89        21.44 

$`FRZB WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        13.15        24.36 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
       88.64        49.25        47.80        56.71        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        26.30         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.18        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       20.19        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  FRZB MUTATED FRZB WILD-TYPE 
          0.16           0.00 
  FRZB MUTATED FRZB WILD-TYPE 
         54.35         223.96 
  FRZB MUTATED FRZB WILD-TYPE 
         19.89          17.92 
[1] "0.2 - 54.4 (19.9)"  "0.0 - 224.0 (17.9)"
[1] "hr=" "1.2"
D388V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FRZB MUTATED         0        1        5         0         2          1
  FRZB WILD-TYPE       4      122      128        46        65         69
                vv
clus             STAGE IIIB STAGE IV
  FRZB MUTATED            0        0
  FRZB WILD-TYPE         11       25
D388V3, multiclass
            clus
vv           FRZB MUTATED FRZB WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              5            128
  STAGE IIA             0             46
  STAGE IIB             2             65
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FRZB MUTATED     1   8   0   0
  FRZB WILD-TYPE 154 253  43  18
D388V4, multiclass
    clus
vv   FRZB MUTATED FRZB WILD-TYPE
  T1            1            154
  T2            8            253
  T3            0             43
  T4            0             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"
                vv
clus              N0  N1 N2+N3
  FRZB MUTATED     6   2     1
  FRZB WILD-TYPE 301  87    71
D388V5, multiclass
       clus
vv      FRZB MUTATED FRZB WILD-TYPE
  N0               6            301
  N1               2             87
  N2+N3            1             71
[1] 3 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
  FRZB MUTATED     8   0
  FRZB WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRZB MUTATED      8    0
  FRZB WILD-TYPE  319   23
   clus
vv  FRZB MUTATED FRZB WILD-TYPE
  0            8            319
  1            0             23
[1] 2 2
[1] FALSE
D388V7, binary
                cls
clus               0   1
  FRZB MUTATED     6   3
  FRZB WILD-TYPE 253 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRZB MUTATED      6    3
  FRZB WILD-TYPE  253  218
        clus
vv       FRZB MUTATED FRZB WILD-TYPE
  FEMALE            6            253
  MALE              3            218
[1] 2 2
[1] FALSE
D388V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FRZB MUTATED                            1                                 3
  FRZB WILD-TYPE                         17                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FRZB MUTATED                                                    2
  FRZB WILD-TYPE                                                292
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FRZB MUTATED                                            0
  FRZB WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FRZB MUTATED                                               1
  FRZB WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  FRZB MUTATED                                0
  FRZB WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  FRZB MUTATED                                    1
  FRZB WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FRZB MUTATED                              0                             1
  FRZB WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FRZB MUTATED                                               0
  FRZB WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  FRZB MUTATED                              0
  FRZB WILD-TYPE                            9
D388V9, multiclass
                                                    clus
vv                                                   FRZB MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   FRZB WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V10, binary
                cls
clus               0   1
  FRZB MUTATED     0   9
  FRZB WILD-TYPE  20 451
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRZB MUTATED      0    9
  FRZB WILD-TYPE   20  451
     clus
vv    FRZB MUTATED FRZB WILD-TYPE
  NO             0             20
  YES            9            451
[1] 2 2
[1] FALSE
D388V11, continuous
D388V12, continuous
                vv
clus              R0  R1  R2  RX
  FRZB MUTATED     7   0   0   0
  FRZB WILD-TYPE 303  11   4  25
D388V13, multiclass
    clus
vv   FRZB MUTATED FRZB WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRZB MUTATED                                  1     0
  FRZB WILD-TYPE                                0     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FRZB MUTATED                           0     7
  FRZB WILD-TYPE                        29   370
D388V14, multiclass
                                  clus
vv                                 FRZB MUTATED FRZB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V15, binary
                cls
clus               0   1
  FRZB MUTATED     0   7
  FRZB WILD-TYPE   6 342
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRZB MUTATED      0    7
  FRZB WILD-TYPE    6  342
                        clus
vv                       FRZB MUTATED FRZB WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            7            342
[1] 2 2
[1] FALSE

Clustering(389) Variable = USP34 MUTATION ANALYSIS
D389V1, survival
                 sevent
clus2               0   1
  USP34 MUTATED    16   6
  USP34 WILD-TYPE 299 135
  USP34 MUTATED USP34 WILD-TYPE 
             22             434 
  USP34 MUTATED USP34 WILD-TYPE 
              6             135 
$`USP34 MUTATED`
TCGA-05-4396 TCGA-05-4424 TCGA-38-4626 TCGA-44-3398 TCGA-50-5049 TCGA-50-6594 
        9.96        30.02       120.79        38.24        70.55        12.16 
TCGA-55-7726 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8620 TCGA-78-7150 
        1.28        17.65        19.82         3.29         2.17        21.90 
TCGA-78-7536 TCGA-78-7539 TCGA-86-8358 TCGA-86-8585 TCGA-91-A4BC TCGA-95-7562 
        8.02        10.75        21.47         1.15         1.45         2.86 
TCGA-95-7947 TCGA-97-7554 TCGA-97-7938 TCGA-MN-A4N1 
       15.68        25.48         0.59        27.19 

$`USP34 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68        97.74        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        13.15        24.36        42.77        37.15 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       17.59        23.64        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.63        12.13        29.26        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       42.35         3.91        25.55        11.05         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
        0.13         3.12         1.32        23.18         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        6.15         0.16        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
       27.16         5.69        19.27        20.58        35.93        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
       26.53        31.20        53.33        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       23.05        14.60        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       14.27         1.18        19.82         9.76         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29         1.12         1.22 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       18.67        12.39        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        5.95         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         3.81         0.20        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  USP34 MUTATED USP34 WILD-TYPE 
           0.59            0.00 
  USP34 MUTATED USP34 WILD-TYPE 
         120.79          223.96 
  USP34 MUTATED USP34 WILD-TYPE 
          13.92           18.15 
[1] "0.6 - 120.8 (13.9)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1"  
D389V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  USP34 MUTATED         0        7        3         5         3          3
  USP34 WILD-TYPE       4      116      130        41        64         67
                 vv
clus              STAGE IIIB STAGE IV
  USP34 MUTATED            1        1
  USP34 WILD-TYPE         10       24
D389V3, multiclass
            clus
vv           USP34 MUTATED USP34 WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             116
  STAGE IB               3             130
  STAGE IIA              5              41
  STAGE IIB              3              64
  STAGE IIIA             3              67
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP34 MUTATED     7  12   3   1
  USP34 WILD-TYPE 148 249  40  17
D389V4, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  T1             7             148
  T2            12             249
  T3             3              40
  T4             1              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"
                 vv
clus               N0  N1 N2+N3
  USP34 MUTATED    15   5     3
  USP34 WILD-TYPE 292  84    69
D389V5, multiclass
       clus
vv      USP34 MUTATED USP34 WILD-TYPE
  N0               15             292
  N1                5              84
  N2+N3             3              69
[1] 3 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
  USP34 MUTATED    17   1
  USP34 WILD-TYPE 310  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     17    1
  USP34 WILD-TYPE  310   22
   clus
vv  USP34 MUTATED USP34 WILD-TYPE
  0            17             310
  1             1              22
[1] 2 2
[1] FALSE
D389V7, binary
                 cls
clus                0   1
  USP34 MUTATED     8  15
  USP34 WILD-TYPE 251 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED      8   15
  USP34 WILD-TYPE  251  206
        clus
vv       USP34 MUTATED USP34 WILD-TYPE
  FEMALE             8             251
  MALE              15             206
[1] 2 2
[1] FALSE
D389V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  USP34 MUTATED                            0                                 5
  USP34 WILD-TYPE                         18                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  USP34 MUTATED                                                   15
  USP34 WILD-TYPE                                                279
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  USP34 MUTATED                                            0
  USP34 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  USP34 MUTATED                                               1
  USP34 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  USP34 MUTATED                                0
  USP34 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  USP34 MUTATED                                    0
  USP34 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  USP34 MUTATED                              0                             1
  USP34 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  USP34 MUTATED                                               1
  USP34 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  USP34 MUTATED                              0
  USP34 WILD-TYPE                            9
D389V9, multiclass
                                                    clus
vv                                                   USP34 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   USP34 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V10, binary
                 cls
clus                0   1
  USP34 MUTATED     2  21
  USP34 WILD-TYPE  18 439
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED      2   21
  USP34 WILD-TYPE   18  439
     clus
vv    USP34 MUTATED USP34 WILD-TYPE
  NO              2              18
  YES            21             439
[1] 2 2
[1] FALSE
D389V11, continuous
D389V12, continuous
                 vv
clus               R0  R1  R2  RX
  USP34 MUTATED    17   1   0   2
  USP34 WILD-TYPE 293  10   4  23
D389V13, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  R0            17             293
  R1             1              10
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP34 MUTATED                                  0     0
  USP34 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP34 MUTATED                           3    17
  USP34 WILD-TYPE                        26   360
D389V14, multiclass
                                  clus
vv                                 USP34 MUTATED USP34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              26
  WHITE                                       17             360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V15, binary
                 cls
clus                0   1
  USP34 MUTATED     0  17
  USP34 WILD-TYPE   6 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED      0   17
  USP34 WILD-TYPE    6  332
                        clus
vv                       USP34 MUTATED USP34 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            17             332
[1] 2 2
[1] FALSE

Clustering(390) Variable = LCK MUTATION ANALYSIS
D390V1, survival
               sevent
clus2             0   1
  LCK MUTATED     8   3
  LCK WILD-TYPE 307 138
  LCK MUTATED LCK WILD-TYPE 
           11           445 
  LCK MUTATED LCK WILD-TYPE 
            3           138 
$`LCK MUTATED`
TCGA-05-4396 TCGA-05-4420 TCGA-55-7907 TCGA-62-8394 TCGA-67-3771 TCGA-78-8662 
        9.96        29.98         0.53         4.57        20.05       110.50 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8358 TCGA-91-6840 TCGA-NJ-A4YP 
        4.57        24.33        21.47        12.23         1.64 

$`LCK WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78         1.45        18.64         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       20.19        19.99        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24         7.04         2.01         0.10 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.52        24.99        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       13.87        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.08         0.79        15.75        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        3.81         0.20        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  LCK MUTATED LCK WILD-TYPE 
         0.53          0.00 
  LCK MUTATED LCK WILD-TYPE 
       110.50        223.96 
  LCK MUTATED LCK WILD-TYPE 
        12.23         18.08 
[1] "0.5 - 110.5 (12.2)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D390V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  LCK MUTATED         0        2        6         1         0          1
  LCK WILD-TYPE       4      121      127        45        67         69
               vv
clus            STAGE IIIB STAGE IV
  LCK MUTATED            2        0
  LCK WILD-TYPE          9       25
D390V3, multiclass
            clus
vv           LCK MUTATED LCK WILD-TYPE
  STAGE I              0             4
  STAGE IA             2           121
  STAGE IB             6           127
  STAGE IIA            1            45
  STAGE IIB            0            67
  STAGE IIIA           1            69
  STAGE IIIB           2             9
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  LCK MUTATED     2   7   0   3
  LCK WILD-TYPE 153 254  43  15
D390V4, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  T1           2           153
  T2           7           254
  T3           0            43
  T4           3            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"
               vv
clus             N0  N1 N2+N3
  LCK MUTATED     9   2     1
  LCK WILD-TYPE 298  87    71
D390V5, multiclass
       clus
vv      LCK MUTATED LCK WILD-TYPE
  N0              9           298
  N1              2            87
  N2+N3           1            71
[1] 3 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
  LCK MUTATED    11   0
  LCK WILD-TYPE 316  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED     11    0
  LCK WILD-TYPE  316   23
   clus
vv  LCK MUTATED LCK WILD-TYPE
  0          11           316
  1           0            23
[1] 2 2
[1] FALSE
D390V7, binary
               cls
clus              0   1
  LCK MUTATED     6   6
  LCK WILD-TYPE 253 215
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      6    6
  LCK WILD-TYPE  253  215
        clus
vv       LCK MUTATED LCK WILD-TYPE
  FEMALE           6           253
  MALE             6           215
[1] 2 2
[1] FALSE
D390V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  LCK MUTATED                            0                                 4
  LCK WILD-TYPE                         18                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  LCK MUTATED                                                    6
  LCK WILD-TYPE                                                288
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  LCK MUTATED                                            0
  LCK WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  LCK MUTATED                                               1
  LCK WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  LCK MUTATED                                0
  LCK WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  LCK MUTATED                                    0                            0
  LCK WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  LCK MUTATED                               1
  LCK WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  LCK MUTATED                                               0
  LCK WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  LCK MUTATED                              0
  LCK WILD-TYPE                            9
D390V9, multiclass
                                                    clus
vv                                                   LCK MUTATED LCK WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           6           288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V10, binary
               cls
clus              0   1
  LCK MUTATED     0  12
  LCK WILD-TYPE  20 448
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      0   12
  LCK WILD-TYPE   20  448
     clus
vv    LCK MUTATED LCK WILD-TYPE
  NO            0            20
  YES          12           448
[1] 2 2
[1] FALSE
D390V11, continuous
D390V12, continuous
               vv
clus             R0  R1  R2  RX
  LCK MUTATED    11   0   0   0
  LCK WILD-TYPE 299  11   4  25
D390V13, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  R0          11           299
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCK MUTATED                                  0     0
  LCK WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LCK MUTATED                           1     7
  LCK WILD-TYPE                        28   370
D390V14, multiclass
                                  clus
vv                                 LCK MUTATED LCK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                      7           370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V15, binary
               cls
clus              0   1
  LCK MUTATED     0   8
  LCK WILD-TYPE   6 341
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      0    8
  LCK WILD-TYPE    6  341
                        clus
vv                       LCK MUTATED LCK WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           8           341
[1] 2 2
[1] FALSE

Clustering(391) Variable = FN1 MUTATION ANALYSIS
D391V1, survival
               sevent
clus2             0   1
  FN1 MUTATED    14   6
  FN1 WILD-TYPE 301 135
  FN1 MUTATED FN1 WILD-TYPE 
           20           436 
  FN1 MUTATED FN1 WILD-TYPE 
            6           135 
$`FN1 MUTATED`
TCGA-05-4427 TCGA-35-4122 TCGA-50-5072 TCGA-55-5899 TCGA-55-6968 TCGA-55-7227 
       26.01         7.40         8.22         2.86        42.51         1.74 
TCGA-55-7724 TCGA-55-8299 TCGA-55-8621 TCGA-55-A4DF TCGA-62-8397 TCGA-64-5781 
       23.18        15.42        16.93        20.19        42.38        51.25 
TCGA-69-A59K TCGA-78-7155 TCGA-86-8073 TCGA-86-8279 TCGA-95-7947 TCGA-95-A4VK 
        7.04        38.50        24.33        15.85        15.68        21.40 
TCGA-99-8025 TCGA-MP-A4SV 
       34.85        86.14 

$`FN1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        14.60        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94         9.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       23.05        48.62         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         3.12         1.32         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61         2.17        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       19.99         4.57        39.98        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       55.43        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
       13.45         4.24         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       29.98        26.30        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       19.43        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
        0.79        15.75        16.08        15.65        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 
        1.22         2.86        18.67        12.39        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
       17.75        20.84        18.67        20.68        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.44        19.00        14.30         3.81         0.20        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63         2.76        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  FN1 MUTATED FN1 WILD-TYPE 
         1.74          0.00 
  FN1 MUTATED FN1 WILD-TYPE 
        86.14        223.96 
  FN1 MUTATED FN1 WILD-TYPE 
       20.795        17.950 
[1] "1.7 - 86.1 (20.8)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D391V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FN1 MUTATED         0        6        6         1         3          4
  FN1 WILD-TYPE       4      117      127        45        64         66
               vv
clus            STAGE IIIB STAGE IV
  FN1 MUTATED            0        1
  FN1 WILD-TYPE         11       24
D391V3, multiclass
            clus
vv           FN1 MUTATED FN1 WILD-TYPE
  STAGE I              0             4
  STAGE IA             6           117
  STAGE IB             6           127
  STAGE IIA            1            45
  STAGE IIB            3            64
  STAGE IIIA           4            66
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FN1 MUTATED     7  10   4   0
  FN1 WILD-TYPE 148 251  39  18
D391V4, multiclass
    clus
vv   FN1 MUTATED FN1 WILD-TYPE
  T1           7           148
  T2          10           251
  T3           4            39
  T4           0            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"
               vv
clus             N0  N1 N2+N3
  FN1 MUTATED    14   4     3
  FN1 WILD-TYPE 293  85    69
D391V5, multiclass
       clus
vv      FN1 MUTATED FN1 WILD-TYPE
  N0             14           293
  N1              4            85
  N2+N3           3            69
[1] 3 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
  FN1 MUTATED    15   1
  FN1 WILD-TYPE 312  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  FN1 MUTATED     15    1
  FN1 WILD-TYPE  312   22
   clus
vv  FN1 MUTATED FN1 WILD-TYPE
  0          15           312
  1           1            22
[1] 2 2
[1] FALSE
D391V7, binary
               cls
clus              0   1
  FN1 MUTATED     9  12
  FN1 WILD-TYPE 250 209
[1] "tbl2"
               cls
clus            [,1] [,2]
  FN1 MUTATED      9   12
  FN1 WILD-TYPE  250  209
        clus
vv       FN1 MUTATED FN1 WILD-TYPE
  FEMALE           9           250
  MALE            12           209
[1] 2 2
[1] FALSE
D391V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FN1 MUTATED                            0                                 6
  FN1 WILD-TYPE                         18                                96
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FN1 MUTATED                                                   13
  FN1 WILD-TYPE                                                281
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FN1 MUTATED                                            0
  FN1 WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FN1 MUTATED                                               1
  FN1 WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  FN1 MUTATED                                0
  FN1 WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  FN1 MUTATED                                    0                            0
  FN1 WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  FN1 MUTATED                               0
  FN1 WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FN1 MUTATED                                               1
  FN1 WILD-TYPE                                             4
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  FN1 MUTATED                              0
  FN1 WILD-TYPE                            9
D391V9, multiclass
                                                    clus
vv                                                   FN1 MUTATED FN1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            6            96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          13           281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                1             4
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V10, binary
               cls
clus              0   1
  FN1 MUTATED     1  20
  FN1 WILD-TYPE  19 440
[1] "tbl2"
               cls
clus            [,1] [,2]
  FN1 MUTATED      1   20
  FN1 WILD-TYPE   19  440
     clus
vv    FN1 MUTATED FN1 WILD-TYPE
  NO            1            19
  YES          20           440
[1] 2 2
[1] FALSE
D391V11, continuous
D391V12, continuous
               vv
clus             R0  R1  R2  RX
  FN1 MUTATED    16   0   0   1
  FN1 WILD-TYPE 294  11   4  24
D391V13, multiclass
    clus
vv   FN1 MUTATED FN1 WILD-TYPE
  R0          16           294
  R1           0            11
  R2           0             4
  RX           1            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FN1 MUTATED                                  0     0
  FN1 WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FN1 MUTATED                           2    16
  FN1 WILD-TYPE                        27   361
D391V14, multiclass
                                  clus
vv                                 FN1 MUTATED FN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  2            27
  WHITE                                     16           361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V15, binary
               cls
clus              0   1
  FN1 MUTATED     0  17
  FN1 WILD-TYPE   6 332
[1] "tbl2"
               cls
clus            [,1] [,2]
  FN1 MUTATED      0   17
  FN1 WILD-TYPE    6  332
                        clus
vv                       FN1 MUTATED FN1 WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          17           332
[1] 2 2
[1] FALSE

Clustering(392) Variable = RUFY2 MUTATION ANALYSIS
D392V1, survival
                 sevent
clus2               0   1
  RUFY2 MUTATED     6   2
  RUFY2 WILD-TYPE 309 139
  RUFY2 MUTATED RUFY2 WILD-TYPE 
              8             448 
  RUFY2 MUTATED RUFY2 WILD-TYPE 
              2             139 
$`RUFY2 MUTATED`
TCGA-05-5425 TCGA-38-4631 TCGA-44-6777 TCGA-44-6778 TCGA-44-7662 TCGA-50-5946 
       29.00        11.64        32.45        61.28         7.17        22.55 
TCGA-73-4670 TCGA-97-A4M5 
        4.31        20.84 

$`RUFY2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        13.15        24.36        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        23.18        63.72        16.44        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       12.13        29.26        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
        8.45        15.12        18.64        29.03        25.12        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24         7.04         2.01         0.10        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       23.38        29.98        26.30        15.35         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         3.81         0.20        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  RUFY2 MUTATED RUFY2 WILD-TYPE 
           4.31            0.00 
  RUFY2 MUTATED RUFY2 WILD-TYPE 
          61.28          223.96 
  RUFY2 MUTATED RUFY2 WILD-TYPE 
         21.695          17.950 
[1] "4.3 - 61.3 (21.7)"  "0.0 - 224.0 (18.0)"
[1] "hr=" "1.3"
D392V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RUFY2 MUTATED         0        3        3         0         1          0
  RUFY2 WILD-TYPE       4      120      130        46        66         70
                 vv
clus              STAGE IIIB STAGE IV
  RUFY2 MUTATED            0        1
  RUFY2 WILD-TYPE         11       24
D392V3, multiclass
            clus
vv           RUFY2 MUTATED RUFY2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               3             130
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUFY2 MUTATED     3   5   0   0
  RUFY2 WILD-TYPE 152 256  43  18
D392V4, multiclass
    clus
vv   RUFY2 MUTATED RUFY2 WILD-TYPE
  T1             3             152
  T2             5             256
  T3             0              43
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  RUFY2 MUTATED     6   1     0
  RUFY2 WILD-TYPE 301  88    72
D392V5, multiclass
       clus
vv      RUFY2 MUTATED RUFY2 WILD-TYPE
  N0                6             301
  N1                1              88
  N2+N3             0              72
[1] 3 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
  RUFY2 MUTATED     3   1
  RUFY2 WILD-TYPE 324  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY2 MUTATED      3    1
  RUFY2 WILD-TYPE  324   22
   clus
vv  RUFY2 MUTATED RUFY2 WILD-TYPE
  0             3             324
  1             1              22
[1] 2 2
[1] FALSE
D392V7, binary
                 cls
clus                0   1
  RUFY2 MUTATED     3   5
  RUFY2 WILD-TYPE 256 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY2 MUTATED      3    5
  RUFY2 WILD-TYPE  256  216
        clus
vv       RUFY2 MUTATED RUFY2 WILD-TYPE
  FEMALE             3             256
  MALE               5             216
[1] 2 2
[1] FALSE
D392V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RUFY2 MUTATED                            0                                 3
  RUFY2 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RUFY2 MUTATED                                                    5
  RUFY2 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RUFY2 MUTATED                                            0
  RUFY2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RUFY2 MUTATED                                               0
  RUFY2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RUFY2 MUTATED                                0
  RUFY2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RUFY2 MUTATED                                    0
  RUFY2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RUFY2 MUTATED                              0                             0
  RUFY2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RUFY2 MUTATED                                               0
  RUFY2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RUFY2 MUTATED                              0
  RUFY2 WILD-TYPE                            9
D392V9, multiclass
                                                    clus
vv                                                   RUFY2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   RUFY2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V10, binary
                 cls
clus                0   1
  RUFY2 MUTATED     1   7
  RUFY2 WILD-TYPE  19 453
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY2 MUTATED      1    7
  RUFY2 WILD-TYPE   19  453
     clus
vv    RUFY2 MUTATED RUFY2 WILD-TYPE
  NO              1              19
  YES             7             453
[1] 2 2
[1] FALSE
D392V11, continuous
D392V12, continuous
                 vv
clus               R0  R1  R2  RX
  RUFY2 MUTATED     3   0   0   0
  RUFY2 WILD-TYPE 307  11   4  25
D392V13, multiclass
    clus
vv   RUFY2 MUTATED RUFY2 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUFY2 MUTATED                                  0     0
  RUFY2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUFY2 MUTATED                           1     6
  RUFY2 WILD-TYPE                        28   371
D392V14, multiclass
                                  clus
vv                                 RUFY2 MUTATED RUFY2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        6             371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V15, binary
                 cls
clus                0   1
  RUFY2 MUTATED     0   4
  RUFY2 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY2 MUTATED      0    4
  RUFY2 WILD-TYPE    6  345
                        clus
vv                       RUFY2 MUTATED RUFY2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(393) Variable = YIPF1 MUTATION ANALYSIS
D393V1, survival
                 sevent
clus2               0   1
  YIPF1 MUTATED     3   0
  YIPF1 WILD-TYPE 312 141
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              3             453 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              0             141 
$`YIPF1 MUTATED`
TCGA-55-7994 TCGA-64-1679 TCGA-73-4670 
       19.82        55.43         4.31 

$`YIPF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        13.15 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       24.36        42.77        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       29.26        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        18.64        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94         9.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        20.65        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        2.30         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        7.04         2.01         0.10        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30        15.35         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       23.51       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      223.96         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        10.75        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         3.81         0.20        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  YIPF1 MUTATED YIPF1 WILD-TYPE 
           4.31            0.00 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
          55.43          223.96 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
          19.82           17.98 
[1] "4.3 - 55.4 (19.8)"  "0.0 - 224.0 (18.0)"
[1] "hr="     "3300000"
D393V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  YIPF1 MUTATED         0        0        0         0         1          1
  YIPF1 WILD-TYPE       4      123      133        46        66         69
                 vv
clus              STAGE IIIB STAGE IV
  YIPF1 MUTATED            0        1
  YIPF1 WILD-TYPE         11       24
D393V3, multiclass
            clus
vv           YIPF1 MUTATED YIPF1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               0             133
  STAGE IIA              0              46
  STAGE IIB              1              66
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YIPF1 MUTATED     1   1   1   0
  YIPF1 WILD-TYPE 154 260  42  18
D393V4, multiclass
    clus
vv   YIPF1 MUTATED YIPF1 WILD-TYPE
  T1             1             154
  T2             1             260
  T3             1              42
  T4             0              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"
                 vv
clus               N0  N1 N2+N3
  YIPF1 MUTATED     2   0     1
  YIPF1 WILD-TYPE 305  89    71
D393V5, multiclass
       clus
vv      YIPF1 MUTATED YIPF1 WILD-TYPE
  N0                2             305
  N1                0              89
  N2+N3             1              71
[1] 3 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
  YIPF1 MUTATED     1   1
  YIPF1 WILD-TYPE 326  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      1    1
  YIPF1 WILD-TYPE  326   22
   clus
vv  YIPF1 MUTATED YIPF1 WILD-TYPE
  0             1             326
  1             1              22
[1] 2 2
[1] FALSE
D393V7, binary
                 cls
clus                0   1
  YIPF1 MUTATED     2   1
  YIPF1 WILD-TYPE 257 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      2    1
  YIPF1 WILD-TYPE  257  220
        clus
vv       YIPF1 MUTATED YIPF1 WILD-TYPE
  FEMALE             2             257
  MALE               1             220
[1] 2 2
[1] FALSE
D393V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  YIPF1 MUTATED                            0                                 0
  YIPF1 WILD-TYPE                         18                               102
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  YIPF1 MUTATED                                                    3
  YIPF1 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  YIPF1 MUTATED                                            0
  YIPF1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  YIPF1 MUTATED                                               0
  YIPF1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  YIPF1 MUTATED                                0
  YIPF1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  YIPF1 MUTATED                                    0
  YIPF1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  YIPF1 MUTATED                              0                             0
  YIPF1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  YIPF1 MUTATED                                               0
  YIPF1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  YIPF1 MUTATED                              0
  YIPF1 WILD-TYPE                            9
D393V9, multiclass
                                                    clus
vv                                                   YIPF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   YIPF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V10, binary
                 cls
clus                0   1
  YIPF1 MUTATED     0   3
  YIPF1 WILD-TYPE  20 457
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      0    3
  YIPF1 WILD-TYPE   20  457
     clus
vv    YIPF1 MUTATED YIPF1 WILD-TYPE
  NO              0              20
  YES             3             457
[1] 2 2
[1] FALSE
D393V11, continuous
D393V12, continuous
[1] "Remove cluster labels:" "YIPF1 MUTATED"         
clus
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              1             256 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6642 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-6712      TCGA-55-6971      TCGA-55-7227      TCGA-55-7283 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7907 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-8089 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-8506      TCGA-55-8507      TCGA-55-8511      TCGA-55-8512 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8615      TCGA-55-8620      TCGA-55-8621 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-A48X      TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-55-A491      TCGA-55-A492      TCGA-55-A493      TCGA-55-A494 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-62-8398      TCGA-64-1677      TCGA-64-1681      TCGA-64-5774 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-69-7761      TCGA-69-7763      TCGA-69-7764      TCGA-69-7765 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7979      TCGA-69-8253      TCGA-69-8255 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4675      TCGA-73-4676      TCGA-73-7498 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7031 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-80-5608      TCGA-83-5908      TCGA-86-6851      TCGA-86-7711 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-8054      TCGA-86-8055 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8281 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8673 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-91-6829      TCGA-91-6830 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7567      TCGA-95-7944      TCGA-95-7947 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8176 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
     TCGA-MP-A5C7      TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" "YIPF1 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  YIPF1 MUTATED     3   0   0   0
  YIPF1 WILD-TYPE 307  11   4  25
D393V13, multiclass
    clus
vv   YIPF1 MUTATED YIPF1 WILD-TYPE
  R0             3             307
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YIPF1 MUTATED                                  0     0
  YIPF1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  YIPF1 MUTATED                           0     3
  YIPF1 WILD-TYPE                        29   374
D393V14, multiclass
                                  clus
vv                                 YIPF1 MUTATED YIPF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        3             374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V15, binary
                 cls
clus                0   1
  YIPF1 MUTATED     0   3
  YIPF1 WILD-TYPE   6 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      0    3
  YIPF1 WILD-TYPE    6  346
                        clus
vv                       YIPF1 MUTATED YIPF1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             346
[1] 2 2
[1] FALSE
